6YX7 | pdb_00006yx7

The high resolution structure of allophycocyanin from cyanobacterium Nostoc sp. WR13, the P21212 crystal form.

PDB DOI: https://doi.org/10.2210/pdb6YX7/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Nostoc sp. WR13
Mutation(s): No

Deposited: 2020-04-30 Released: 2021-05-12
Deposition Author(s): Patel, H.M., Roszak, A.W., Madamwar, D., Cogdell, R.J.
Funding Organization(s): Department of Energy (DOE, United States), Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free:
0.175 (Depositor), 0.184 (DCC)
R-Value Work:
0.126 (Depositor), 0.141 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The high resolution structure of allophycocyanin from cyanobacterium Nostoc sp. WR13

Patel, H.M., Roszak, A.W., Madamwar, D., Cogdell, R.J.

To be published.

Macromolecule Content

Total Structure Weight: 218.01 kDa
Atom Count: 19,418
Modeled Residue Count: 1,926
Deposited Residue Count: 1,926
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Allophycocyanin alpha	A [auth AAA] C [auth CCC] E [auth EEE] G [auth GGG] I [auth III] A [auth AAA], C [auth CCC], E [auth EEE], G [auth GGG], I [auth III], K [auth KKK]	160	Nostoc sp. WR13	Mutation(s): 0
UniProt
Find proteins for A0A4Y5PW22 (Nostoc sp. WR13) Explore A0A4Y5PW22 Go to UniProtKB: A0A4Y5PW22
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A4Y5PW22
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Allophycocyanin beta	B [auth BBB] D [auth DDD] F [auth FFF] H [auth HHH] J [auth JJJ] B [auth BBB], D [auth DDD], F [auth FFF], H [auth HHH], J [auth JJJ], L [auth LLL]	161	Nostoc sp. WR13	Mutation(s): 0
UniProt
Find proteins for A0A4Y5PW23 (Nostoc sp. WR13) Explore A0A4Y5PW23 Go to UniProtKB: A0A4Y5PW23
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A4Y5PW23
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 14 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CYC (Subject of Investigation/LOI) Query on CYC Download:Ideal Coordinates CCD File SDF format, chain M [auth AAA] SDF format, chain MA [auth GGG] SDF format, chain O [auth BBB] SDF format, chain VA [auth III] SDF format, chain W [auth CCC] SDF format, chain XA [auth JJJ] SDF format, chain RA [auth HHH] SDF format, chain IA [auth FFF] SDF format, chain GB [auth LLL] SDF format, chain FA [auth EEE] SDF format, chain CB [auth KKK] SDF format, chain CA [auth DDD] MOL2 format, chain M [auth AAA] MOL2 format, chain MA [auth GGG] MOL2 format, chain O [auth BBB] MOL2 format, chain VA [auth III] MOL2 format, chain W [auth CCC] MOL2 format, chain XA [auth JJJ] MOL2 format, chain RA [auth HHH] MOL2 format, chain IA [auth FFF] MOL2 format, chain GB [auth LLL] MOL2 format, chain FA [auth EEE] MOL2 format, chain CB [auth KKK] MOL2 format, chain CA [auth DDD] mmCIF format, chain M [auth AAA] mmCIF format, chain MA [auth GGG] mmCIF format, chain O [auth BBB] mmCIF format, chain VA [auth III] mmCIF format, chain W [auth CCC] mmCIF format, chain XA [auth JJJ] mmCIF format, chain RA [auth HHH] mmCIF format, chain IA [auth FFF] mmCIF format, chain GB [auth LLL] mmCIF format, chain FA [auth EEE] mmCIF format, chain CB [auth KKK] mmCIF format, chain CA [auth DDD]	CA [auth DDD] CB [auth KKK] FA [auth EEE] GB [auth LLL] IA [auth FFF] CA [auth DDD], CB [auth KKK], FA [auth EEE], GB [auth LLL], IA [auth FFF], M [auth AAA], MA [auth GGG], O [auth BBB], RA [auth HHH], VA [auth III], W [auth CCC], XA [auth JJJ]	PHYCOCYANOBILIN C₃₃ H₄₀ N₄ O₆ VXTXPYZGDQPMHK-GMXXPEQVSA-N		Interactions Focus chain CA [auth DDD] Focus chain CB [auth KKK] Focus chain FA [auth EEE] Focus chain GB [auth LLL] Focus chain IA [auth FFF] Focus chain M [auth AAA] Focus chain MA [auth GGG] Focus chain O [auth BBB] Focus chain RA [auth HHH] Focus chain VA [auth III] Focus chain W [auth CCC] Focus chain XA [auth JJJ] Interactions & Density Focus chain CA [auth DDD] Focus chain CB [auth KKK] Focus chain FA [auth EEE] Focus chain GB [auth LLL] Focus chain IA [auth FFF] Focus chain M [auth AAA] Focus chain MA [auth GGG] Focus chain O [auth BBB] Focus chain RA [auth HHH] Focus chain VA [auth III] Focus chain W [auth CCC] Focus chain XA [auth JJJ]
P6G Query on P6G Download:Ideal Coordinates CCD File SDF format, chain X [auth CCC] MOL2 format, chain X [auth CCC] mmCIF format, chain X [auth CCC]	X [auth CCC]	HEXAETHYLENE GLYCOL C₁₂ H₂₆ O₇ IIRDTKBZINWQAW-UHFFFAOYSA-N		Interactions Focus chain X [auth CCC] Interactions & Density Focus chain X [auth CCC]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain R [auth BBB] MOL2 format, chain R [auth BBB] mmCIF format, chain R [auth BBB]	R [auth BBB]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain R [auth BBB] Interactions & Density Focus chain R [auth BBB]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain N [auth AAA] SDF format, chain Y [auth CCC] SDF format, chain LA [auth FFF] SDF format, chain AB [auth JJJ] MOL2 format, chain N [auth AAA] MOL2 format, chain Y [auth CCC] MOL2 format, chain LA [auth FFF] MOL2 format, chain AB [auth JJJ] mmCIF format, chain N [auth AAA] mmCIF format, chain Y [auth CCC] mmCIF format, chain LA [auth FFF] mmCIF format, chain AB [auth JJJ]	AB [auth JJJ], LA [auth FFF], N [auth AAA], Y [auth CCC]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain AB [auth JJJ] Focus chain LA [auth FFF] Focus chain N [auth AAA] Focus chain Y [auth CCC] Interactions & Density Focus chain AB [auth JJJ] Focus chain LA [auth FFF] Focus chain N [auth AAA] Focus chain Y [auth CCC]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain OA [auth GGG] SDF format, chain PA [auth GGG] SDF format, chain JB [auth LLL] MOL2 format, chain OA [auth GGG] MOL2 format, chain PA [auth GGG] MOL2 format, chain JB [auth LLL] mmCIF format, chain OA [auth GGG] mmCIF format, chain PA [auth GGG] mmCIF format, chain JB [auth LLL]	JB [auth LLL], OA [auth GGG], PA [auth GGG]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain JB [auth LLL] Focus chain OA [auth GGG] Focus chain PA [auth GGG] Interactions & Density Focus chain JB [auth LLL] Focus chain OA [auth GGG] Focus chain PA [auth GGG]
LYS Query on LYS Download:Ideal Coordinates CCD File SDF format, chain DB [auth KKK] SDF format, chain P [auth BBB] SDF format, chain WA [auth III] MOL2 format, chain DB [auth KKK] MOL2 format, chain P [auth BBB] MOL2 format, chain WA [auth III] mmCIF format, chain DB [auth KKK] mmCIF format, chain P [auth BBB] mmCIF format, chain WA [auth III]	DB [auth KKK], P [auth BBB], WA [auth III]	LYSINE C₆ H₁₅ N₂ O₂ KDXKERNSBIXSRK-YFKPBYRVSA-O		Interactions Focus chain DB [auth KKK] Focus chain P [auth BBB] Focus chain WA [auth III] Interactions & Density Focus chain DB [auth KKK] Focus chain P [auth BBB] Focus chain WA [auth III]
GLU Query on GLU Download:Ideal Coordinates CCD File SDF format, chain DA [auth DDD] SDF format, chain SA [auth HHH] MOL2 format, chain DA [auth DDD] MOL2 format, chain SA [auth HHH] mmCIF format, chain DA [auth DDD] mmCIF format, chain SA [auth HHH]	DA [auth DDD], SA [auth HHH]	GLUTAMIC ACID C₅ H₉ N O₄ WHUUTDBJXJRKMK-VKHMYHEASA-N		Interactions Focus chain DA [auth DDD] Focus chain SA [auth HHH] Interactions & Density Focus chain DA [auth DDD] Focus chain SA [auth HHH]
MRD Query on MRD Download:Ideal Coordinates CCD File SDF format, chain NA [auth GGG] MOL2 format, chain NA [auth GGG] mmCIF format, chain NA [auth GGG]	NA [auth GGG]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain NA [auth GGG] Interactions & Density Focus chain NA [auth GGG]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain EA [auth DDD] SDF format, chain KA [auth FFF] SDF format, chain TA [auth HHH] SDF format, chain ZA [auth JJJ] SDF format, chain Q [auth BBB] SDF format, chain IB [auth LLL] SDF format, chain HA [auth EEE] MOL2 format, chain EA [auth DDD] MOL2 format, chain KA [auth FFF] MOL2 format, chain TA [auth HHH] MOL2 format, chain ZA [auth JJJ] MOL2 format, chain Q [auth BBB] MOL2 format, chain IB [auth LLL] MOL2 format, chain HA [auth EEE] mmCIF format, chain EA [auth DDD] mmCIF format, chain KA [auth FFF] mmCIF format, chain TA [auth HHH] mmCIF format, chain ZA [auth JJJ] mmCIF format, chain Q [auth BBB] mmCIF format, chain IB [auth LLL] mmCIF format, chain HA [auth EEE]	EA [auth DDD] HA [auth EEE] IB [auth LLL] KA [auth FFF] Q [auth BBB] EA [auth DDD], HA [auth EEE], IB [auth LLL], KA [auth FFF], Q [auth BBB], TA [auth HHH], ZA [auth JJJ]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain EA [auth DDD] Focus chain HA [auth EEE] Focus chain IB [auth LLL] Focus chain KA [auth FFF] Focus chain Q [auth BBB] Focus chain TA [auth HHH] Focus chain ZA [auth JJJ] Interactions & Density Focus chain EA [auth DDD] Focus chain HA [auth EEE] Focus chain IB [auth LLL] Focus chain KA [auth FFF] Focus chain Q [auth BBB] Focus chain TA [auth HHH] Focus chain ZA [auth JJJ]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain S [auth BBB] SDF format, chain UA [auth HHH] SDF format, chain Z [auth CCC] SDF format, chain V [auth BBB] SDF format, chain T [auth BBB] SDF format, chain QA [auth GGG] SDF format, chain BB [auth JJJ] MOL2 format, chain S [auth BBB] MOL2 format, chain UA [auth HHH] MOL2 format, chain Z [auth CCC] MOL2 format, chain V [auth BBB] MOL2 format, chain T [auth BBB] MOL2 format, chain QA [auth GGG] MOL2 format, chain BB [auth JJJ] mmCIF format, chain S [auth BBB] mmCIF format, chain UA [auth HHH] mmCIF format, chain Z [auth CCC] mmCIF format, chain V [auth BBB] mmCIF format, chain T [auth BBB] mmCIF format, chain QA [auth GGG] mmCIF format, chain BB [auth JJJ]	BB [auth JJJ] QA [auth GGG] S [auth BBB] T [auth BBB] UA [auth HHH] BB [auth JJJ], QA [auth GGG], S [auth BBB], T [auth BBB], UA [auth HHH], V [auth BBB], Z [auth CCC]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain BB [auth JJJ] Focus chain QA [auth GGG] Focus chain S [auth BBB] Focus chain T [auth BBB] Focus chain UA [auth HHH] Focus chain V [auth BBB] Focus chain Z [auth CCC] Interactions & Density Focus chain BB [auth JJJ] Focus chain QA [auth GGG] Focus chain S [auth BBB] Focus chain T [auth BBB] Focus chain UA [auth HHH] Focus chain V [auth BBB] Focus chain Z [auth CCC]
DSN Query on DSN Download:Ideal Coordinates CCD File SDF format, chain HB [auth LLL] SDF format, chain YA [auth JJJ] MOL2 format, chain HB [auth LLL] MOL2 format, chain YA [auth JJJ] mmCIF format, chain HB [auth LLL] mmCIF format, chain YA [auth JJJ]	HB [auth LLL], YA [auth JJJ]	D-SERINE C₃ H₇ N O₃ MTCFGRXMJLQNBG-UWTATZPHSA-N		Interactions Focus chain HB [auth LLL] Focus chain YA [auth JJJ] Interactions & Density Focus chain HB [auth LLL] Focus chain YA [auth JJJ]
ALA Query on ALA Download:Ideal Coordinates CCD File SDF format, chain JA [auth FFF] MOL2 format, chain JA [auth FFF] mmCIF format, chain JA [auth FFF]	JA [auth FFF]	ALANINE C₃ H₇ N O₂ QNAYBMKLOCPYGJ-REOHCLBHSA-N		Interactions Focus chain JA [auth FFF] Interactions & Density Focus chain JA [auth FFF]
GLY Query on GLY Download:Ideal Coordinates CCD File SDF format, chain GA [auth EEE] MOL2 format, chain GA [auth EEE] mmCIF format, chain GA [auth EEE]	GA [auth EEE]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain GA [auth EEE] Interactions & Density Focus chain GA [auth EEE]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AA [auth CCC] SDF format, chain BA [auth CCC] SDF format, chain EB [auth KKK] SDF format, chain U [auth BBB] SDF format, chain FB [auth KKK] MOL2 format, chain AA [auth CCC] MOL2 format, chain BA [auth CCC] MOL2 format, chain EB [auth KKK] MOL2 format, chain U [auth BBB] MOL2 format, chain FB [auth KKK] mmCIF format, chain AA [auth CCC] mmCIF format, chain BA [auth CCC] mmCIF format, chain EB [auth KKK] mmCIF format, chain U [auth BBB] mmCIF format, chain FB [auth KKK]	AA [auth CCC], BA [auth CCC], EB [auth KKK], FB [auth KKK], U [auth BBB]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth CCC] Focus chain BA [auth CCC] Focus chain EB [auth KKK] Focus chain FB [auth KKK] Focus chain U [auth BBB] Interactions & Density Focus chain AA [auth CCC] Focus chain BA [auth CCC] Focus chain EB [auth KKK] Focus chain FB [auth KKK] Focus chain U [auth BBB]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MEN Query on MEN	B [auth BBB] D [auth DDD] F [auth FFF] H [auth HHH] J [auth JJJ] B [auth BBB], D [auth DDD], F [auth FFF], H [auth HHH], J [auth JJJ], L [auth LLL]	L-PEPTIDE LINKING	C₅ H₁₀ N₂ O₃		ASN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.42 Å
R-Value Free: 0.175 (Depositor), 0.184 (DCC)
R-Value Work: 0.126 (Depositor), 0.141 (DCC)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.695	α = 90
b = 177.726	β = 90
c = 106.372	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
autoPROC	data scaling
STARANISO	data scaling
PHASER	phasing
Coot	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-05-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-SC0001035 (Office of Basic Energy Sciences)
Department of Biotechnology (DBT, India)	India	BT/PR15686/AAQ/3/811/2016 (UGC-BSR Faculty Fellowship)
Department of Biotechnology (DBT, India)	India	BT/IN/UK/DBT-BC/2017-18 (Newton-Bhabha fellowship)

Revision History (Full details and data files)

Version 1.0: 2021-05-12
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Derived calculations, Refinement description