3BDK | pdb_00003bdk

Crystal Structure of Streptococcus suis mannonate dehydratase complexed with substrate analogue

• PDB DOI: https://doi.org/10.2210/pdb3BDK/pdb

• Classification: LYASE
• Organism(s): Streptococcus suis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-11-15 Released: 2008-11-18 
• Deposition Author(s): Gao, F., Zhang, Q.M., Peng, H., Liu, Y.W., Qi, J.X., Gao, G.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.303 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.250 (Depositor) 
• R-Value Observed: 
  0.253 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Streptococcus suis mannonate dehydratase complexed with substrate analogue

Gao, F., Zhang, Q.M., Peng, H., Liu, Y.W., Qi, J.X., Gao, G.F.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 86.28 kDa 
• Atom Count: 5,525 
• Modeled Residue Count: 698 
• Deposited Residue Count: 772 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-mannonate dehydratase	A, B	386	Streptococcus suis	Mutation(s): 0  Gene Names: UxuA EC: 4.2.1.8
UniProt
Find proteins for A4VVI4 (Streptococcus suis (strain 05ZYH33)) Explore A4VVI4  Go to UniProtKB:  A4VVI4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DNO	C [auth A]	D-mannose C6 H12 O6 GZCGUPFRVQAUEE-KVTDHHQDSA-N
MN	D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.303 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.250 (Depositor) 
• R-Value Observed: 0.253 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.468	α = 90
b = 105.468	β = 90
c = 160.155	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-11-18 
Deposition Author(s): Gao, F., Zhang, Q.M., Peng, H., Liu, Y.W., Qi, J.X., Gao, G.F.

Revision History  

• Version 1.0: 2008-11-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description