3PRU | pdb_00003pru

Crystal Structure of Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1 (fragment 14-158) from Synechocystis sp. PCC 6803, Northeast Structural Genomics Consortium Target SgR182A

PDB DOI: https://doi.org/10.2210/pdb3PRU/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Synechocystis sp. PCC 6803
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-11-30 Released: 2010-12-15
Deposition Author(s): Kuzin, A., Su, M., Patel, P., Xiao, R., Ciccosanti, C., Lee, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.68 Å
R-Value Free:
0.241 (Depositor), 0.235 (DCC)
R-Value Work:
0.193 (Depositor), 0.191 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Northeast Structural Genomics Consortium Target SgR182A

Kuzin, A., Su, M., Patel, P., Xiao, R., Ciccosanti, C., Lee, D., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 73.61 kDa
Atom Count: 4,729
Modeled Residue Count: 558
Deposited Residue Count: 616
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1	A [auth C], B [auth A], C [auth B], D	154	Synechocystis sp. PCC 6803	Mutation(s): 0 Gene Names: cpcC1, sll1580
UniProt
Find proteins for P73203 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P73203 Go to UniProtKB: P73203
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P73203
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain E [auth C] MOL2 format, chain E [auth C] mmCIF format, chain E [auth C]	E [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth C] Interactions & Density Focus chain E [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A [auth C], B [auth A], C [auth B], D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.68 Å
R-Value Free: 0.241 (Depositor), 0.235 (DCC)
R-Value Work: 0.193 (Depositor), 0.191 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.354	α = 90
b = 91.532	β = 90
c = 124.673	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
BALBES	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-12-15

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2010-12-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-02-22
Changes: Structure summary
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2023-12-06
Changes: Data collection
Version 1.5: 2024-11-06
Changes: Structure summary