4BK9 | pdb_00004bk9

Crystal structure of 2-keto-3-deoxy-6-phospho-gluconate aldolase from Zymomonas mobilis ATCC 29191

PDB DOI: https://doi.org/10.2210/pdb4BK9/pdb

Classification: LYASE
Organism(s): Zymomonas mobilis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-04-22 Released: 2014-04-30
Deposition Author(s): Classen, T., Schlieper, D., Groth, G., Pietruszka, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.77 Å
R-Value Free:
0.172 (Depositor), 0.181 (DCC)
R-Value Work:
0.135 (Depositor), 0.146 (DCC)
R-Value Observed:
0.137 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of 2-Keto-3-Deoxy-6-Phospho- Gluconate Aldolase from Zymomonas Mobilis

Classen, T., Schlieper, D., Groth, G., Pietruszka, J.

To be published.

Macromolecule Content

Total Structure Weight: 68.48 kDa
Atom Count: 4,617
Modeled Residue Count: 620
Deposited Residue Count: 648
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2-DEHYDRO-3-DEOXYPHOSPHOGLUCONATE ALDOLASE/4-HYDROXY-2-OXO GLUTARATE ALDOLASE	A, B, C	216	Zymomonas mobilis	Mutation(s): 0 EC: 4.1.2.14

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain G [auth B] SDF format, chain F [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth B] G [auth B] H [auth B] D [auth A], E [auth A], F [auth B], G [auth B], H [auth B], I [auth B], J [auth C], K [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth C] Focus chain K [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.77 Å
R-Value Free: 0.172 (Depositor), 0.181 (DCC)
R-Value Work: 0.135 (Depositor), 0.146 (DCC)
R-Value Observed: 0.137 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.38	α = 90
b = 118.05	β = 109.51
c = 55.91	γ = 90

Software Package:

Software Name	Purpose
REFMAC	model building
XPREP	data scaling
MrBUMP	phasing
CHAINSAW	phasing
PHASER	phasing
REFMAC	phasing
REFMAC	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-04-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-04-30
Type: Initial release
Version 1.1: 2019-05-08
Changes: Data collection, Experimental preparation, Other
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description