3QM3 | pdb_00003qm3

1.85 Angstrom Resolution Crystal Structure of Fructose-bisphosphate Aldolase (Fba) from Campylobacter jejuni

PDB DOI: https://doi.org/10.2210/pdb3QM3/pdb

Classification: LYASE
Organism(s): Campylobacter jejuni
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-02-03 Released: 2011-02-23
Deposition Author(s): Minasov, G., Wawrzak, Z., Skarina, T., Onopriyenko, O., Papazisi, L., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.191 (Depositor), 0.204 (DCC)
R-Value Work:
0.149 (Depositor), 0.163 (DCC)
R-Value Observed:
0.151 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

1.85 Angstrom Resolution Crystal Structure of Fructose-bisphosphate Aldolase (Fba) from Campylobacter jejuni

Minasov, G., Wawrzak, Z., Skarina, T., Onopriyenko, O., Papazisi, L., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 315.65 kDa
Atom Count: 25,480
Modeled Residue Count: 2,764
Deposited Residue Count: 2,856
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose-bisphosphate aldolase	A, B, C, D, E A, B, C, D, E, F, G, H	357	Campylobacter jejuni	Mutation(s): 0 Gene Names: Cj0597, fba, fda, fdaC EC: 4.1.2.13
UniProt
Find proteins for Q0PAS0 (Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)) Explore Q0PAS0 Go to UniProtKB: Q0PAS0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q0PAS0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain VA [auth H] SDF format, chain V [auth C] SDF format, chain UA [auth H] SDF format, chain U [auth C] SDF format, chain RA [auth G] SDF format, chain R [auth B] SDF format, chain QA [auth G] SDF format, chain Q [auth B] SDF format, chain PA [auth G] SDF format, chain P [auth B] SDF format, chain OA [auth G] SDF format, chain MA [auth F] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain IA [auth E] SDF format, chain HA [auth E] SDF format, chain GA [auth E] SDF format, chain FA [auth E] SDF format, chain CA [auth D] SDF format, chain BA [auth D] MOL2 format, chain W [auth C] MOL2 format, chain VA [auth H] MOL2 format, chain V [auth C] MOL2 format, chain UA [auth H] MOL2 format, chain U [auth C] MOL2 format, chain RA [auth G] MOL2 format, chain R [auth B] MOL2 format, chain QA [auth G] MOL2 format, chain Q [auth B] MOL2 format, chain PA [auth G] MOL2 format, chain P [auth B] MOL2 format, chain OA [auth G] MOL2 format, chain MA [auth F] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain HA [auth E] MOL2 format, chain GA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain CA [auth D] MOL2 format, chain BA [auth D] mmCIF format, chain W [auth C] mmCIF format, chain VA [auth H] mmCIF format, chain V [auth C] mmCIF format, chain UA [auth H] mmCIF format, chain U [auth C] mmCIF format, chain RA [auth G] mmCIF format, chain R [auth B] mmCIF format, chain QA [auth G] mmCIF format, chain Q [auth B] mmCIF format, chain PA [auth G] mmCIF format, chain P [auth B] mmCIF format, chain OA [auth G] mmCIF format, chain MA [auth F] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain IA [auth E] mmCIF format, chain HA [auth E] mmCIF format, chain GA [auth E] mmCIF format, chain FA [auth E] mmCIF format, chain CA [auth D] mmCIF format, chain BA [auth D]	BA [auth D] CA [auth D] FA [auth E] GA [auth E] HA [auth E] BA [auth D], CA [auth D], FA [auth E], GA [auth E], HA [auth E], IA [auth E], K [auth A], L [auth A], MA [auth F], OA [auth G], P [auth B], PA [auth G], Q [auth B], QA [auth G], R [auth B], RA [auth G], U [auth C], UA [auth H], V [auth C], VA [auth H], W [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain MA [auth F] Focus chain OA [auth G] Focus chain P [auth B] Focus chain PA [auth G] Focus chain Q [auth B] Focus chain QA [auth G] Focus chain R [auth B] Focus chain RA [auth G] Focus chain U [auth C] Focus chain UA [auth H] Focus chain V [auth C] Focus chain VA [auth H] Focus chain W [auth C] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain K [auth A] Focus chain L [auth A] Focus chain MA [auth F] Focus chain OA [auth G] Focus chain P [auth B] Focus chain PA [auth G] Focus chain Q [auth B] Focus chain QA [auth G] Focus chain R [auth B] Focus chain RA [auth G] Focus chain U [auth C] Focus chain UA [auth H] Focus chain V [auth C] Focus chain VA [auth H] Focus chain W [auth C]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain T [auth C] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain LA [auth F] SDF format, chain EA [auth E] MOL2 format, chain T [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain LA [auth F] MOL2 format, chain EA [auth E] mmCIF format, chain T [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain LA [auth F] mmCIF format, chain EA [auth E]	EA [auth E], LA [auth F], N [auth B], O [auth B], T [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth E] Focus chain LA [auth F] Focus chain N [auth B] Focus chain O [auth B] Focus chain T [auth C] Interactions & Density Focus chain EA [auth E] Focus chain LA [auth F] Focus chain N [auth B] Focus chain O [auth B] Focus chain T [auth C]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain SA [auth H] SDF format, chain S [auth C] SDF format, chain NA [auth G] SDF format, chain M [auth B] SDF format, chain JA [auth F] SDF format, chain I [auth A] SDF format, chain DA [auth E] MOL2 format, chain X [auth D] MOL2 format, chain SA [auth H] MOL2 format, chain S [auth C] MOL2 format, chain NA [auth G] MOL2 format, chain M [auth B] MOL2 format, chain JA [auth F] MOL2 format, chain I [auth A] MOL2 format, chain DA [auth E] mmCIF format, chain X [auth D] mmCIF format, chain SA [auth H] mmCIF format, chain S [auth C] mmCIF format, chain NA [auth G] mmCIF format, chain M [auth B] mmCIF format, chain JA [auth F] mmCIF format, chain I [auth A] mmCIF format, chain DA [auth E]	DA [auth E] I [auth A] JA [auth F] M [auth B] NA [auth G] DA [auth E], I [auth A], JA [auth F], M [auth B], NA [auth G], S [auth C], SA [auth H], X [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Focus chain I [auth A] Focus chain JA [auth F] Focus chain M [auth B] Focus chain NA [auth G] Focus chain S [auth C] Focus chain SA [auth H] Focus chain X [auth D] Interactions & Density Focus chain DA [auth E] Focus chain I [auth A] Focus chain JA [auth F] Focus chain M [auth B] Focus chain NA [auth G] Focus chain S [auth C] Focus chain SA [auth H] Focus chain X [auth D]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain TA [auth H] SDF format, chain KA [auth F] SDF format, chain J [auth A] SDF format, chain AA [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain TA [auth H] MOL2 format, chain KA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain AA [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain TA [auth H] mmCIF format, chain KA [auth F] mmCIF format, chain J [auth A] mmCIF format, chain AA [auth D]	AA [auth D], J [auth A], KA [auth F], TA [auth H], Z [auth D]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain J [auth A] Focus chain KA [auth F] Focus chain TA [auth H] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain J [auth A] Focus chain KA [auth F] Focus chain TA [auth H] Focus chain Z [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Y [auth D] MOL2 format, chain Y [auth D] mmCIF format, chain Y [auth D]	Y [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain Y [auth D] Interactions & Density Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.191 (Depositor), 0.204 (DCC)
R-Value Work: 0.149 (Depositor), 0.163 (DCC)
R-Value Observed: 0.151 (Depositor)

Diffraction Data:

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.996	α = 113.27
b = 101.971	β = 95.34
c = 105.662	γ = 95.75

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-02-23

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2011-02-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description