2V38 | pdb_00002v38

Family 5 endoglucanase Cel5A from Bacillus agaradhaerens in complex with cellobio-derived noeuromycin

• PDB DOI: https://doi.org/10.2210/pdb2V38/pdb

• Classification: HYDROLASE
• Organism(s): Salipaludibacillus agaradhaerens
• Expression System: Bacillus subtilis
• Mutation(s): No 


• Deposited: 2007-06-13 Released: 2007-06-26 
• Deposition Author(s): Gloster, T.M., Meloncelli, P.J., Money, V.A., Tarling, C.A., Davies, G.J., Withers, S.G., Stick, R.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.143 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.111 (Depositor), 0.120 (DCC) 
• R-Value Observed: 
  0.113 (Depositor) 

Starting Model: experimental

Literature

D-Glucosylated Derivatives of Isofagomine and Noeuromycin and Their Potential as Inhibitors of Beta-Glycoside Hydrolases

Meloncelli, P.J., Gloster, T.M., Money, V.A., Tarling, C.A., Davies, G.J., Withers, S.G., Stick, R.V.

To be published.

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: 34.88 kDa 
• Atom Count: 2,963 
• Modeled Residue Count: 301 
• Deposited Residue Count: 305 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDOGLUCANASE 5A	A	305	Salipaludibacillus agaradhaerens	Mutation(s): 0  EC: 3.2.1.4
UniProt
Find proteins for O85465 (Salipaludibacillus agaradhaerens) Explore O85465  Go to UniProtKB:  O85465

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IDR	G [auth A]	alpha-L-idopyranuronic acid C6 H10 O7 AEMOLEFTQBMNLQ-VCSGLWQLSA-N
IFL	F [auth A]	(3S,4R,5R)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)PIPERIDIN-2-ONE C6 H11 N O4 ARBXEMIAJIJEQI-WDCZJNDASA-N
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	B [auth A], C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.143 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.111 (Depositor), 0.120 (DCC) 
• R-Value Observed: 0.113 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.861	α = 90
b = 69.595	β = 90
c = 76.719	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-26 
Deposition Author(s): Gloster, T.M., Meloncelli, P.J., Money, V.A., Tarling, C.A., Davies, G.J., Withers, S.G., Stick, R.V.

Revision History  

• Version 1.0: 2007-06-26
  Type: Initial release
  
• Version 1.1: 2011-06-02
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Other, Structure summary
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Refinement description, Structure summary