1GVY | pdb_00001gvy

Substrate distorsion by beta-mannanase from Pseudomonas cellulosa

• PDB DOI: https://doi.org/10.2210/pdb1GVY/pdb

• Classification: HYDROLASE
• Organism(s): Cellvibrio japonicus
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2002-02-28 Released: 2002-09-05 
• Deposition Author(s): Ducros, V., Zechel, D.L., Gilbert, H.J., Szabo, L., Withers, S.G., Davies, G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.170 (Depositor) 
• R-Value Work: 
  0.144 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Starting Model: experimental

Literature

Substrate Distortion by a Beta-Mannanase: Snapshots of the Michaelis and Covalent-Intermediate Complexes Suggest a B2,5 Conformation for the Transition State

Ducros, V., Zechel, D.L., Murshudov, G., Gilbert, H.J., Szabo, L., Stoll, D., Withers, S.G., Davies, G.J.

(2002) Angew Chem Int Ed Engl 41: 2824

• PubMed: 12203498 
• DOI: https://doi.org/10.1002/1521-3773(20020802)41:15<2824::AID-ANIE2824>3.0.CO;2-G
• Primary Citation Related Structures: 
  1GVY, 1GW1

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Organizational Affiliation: 
• Department of Chemistry, Structural Biology Laboratory, The University of York, Heslington, York, YO10 5DD, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 44.4 kDa 
• Atom Count: 3,543 
• Modeled Residue Count: 376 
• Deposited Residue Count: 383 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MANNAN ENDO-1,4-BETA-MANNOSIDASE	A	383	Cellvibrio japonicus	Mutation(s): 1  EC: 3.2.1.78
UniProt
Find proteins for P49424 (Cellvibrio japonicus (strain Ueda107)) Explore P49424  Go to UniProtKB:  P49424

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-2-deoxy-2-fluoro-beta-D-mannopyranose	B	3		N/A
Glycosylation Resources
GlyTouCan: G83706MU GlyCosmos: G83706MU

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NIN	C [auth A]	DINITROPHENYLENE C6 H4 N2 O4 WDCYWAQPCXBPJA-UHFFFAOYSA-N
TRS	G [auth A], H [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
ZN	D [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.170 (Depositor) 
• R-Value Work:  0.144 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.192	α = 90
b = 93.192	β = 90
c = 54.343	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-09-05 
Deposition Author(s): Ducros, V., Zechel, D.L., Gilbert, H.J., Szabo, L., Withers, S.G., Davies, G.J.

Revision History  

• Version 1.0: 2002-09-05
  Type: Initial release
  
• Version 1.1: 2016-12-14
  Changes: Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2023-12-13
  Changes: Data collection, Database references, Refinement description, Structure summary