4Q2B

The crystal structure of an endo-1,4-D-glucanase from Pseudomonas putida KT2440

• PDB DOI: https://doi.org/10.2210/pdb4Q2B/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas putida KT2440
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-04-07 Released: 2014-06-25 
• Deposition Author(s): Tan, K., Joachimiak, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 0.198 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 

Literature

The crystal structure of an endo-1,4-D-glucanase from Pseudomonas putida KT2440

Tan, K., Joachimiak, G., Endres, M., Joachimiak, A.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 235.39 kDa 
• Atom Count: 17,169 
• Modelled Residue Count: 2,058 
• Deposited Residue Count: 2,094 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-1,4-beta-D-glucanase	A, B, C, D, E, F	349	Pseudomonas putida KT2440	Mutation(s): 0  Gene Names: PP_2637 EC: 3.2.1
UniProt
Find proteins for Q88JL2 (Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)) Explore Q88JL2  Go to UniProtKB:  Q88JL2

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	CA [auth E], EA [auth F], H [auth A], Z [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
MLA	Q [auth C]	MALONIC ACID C3 H4 O4 OFOBLEOULBTSOW-UHFFFAOYSA-N
SO4	BA [auth E], DA [auth F], G [auth A], L [auth B], O [auth C], P [auth C], X [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	R [auth C], S [auth C], Y [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	W [auth C]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
FMT	AA [auth D], I [auth A], J [auth A], K [auth A], M [auth B], N [auth B], T [auth C], U [auth C], V [auth C]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D, E, F	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 0.198 
• R-Value Work: 0.163 
• R-Value Observed: 0.165 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.938	α = 90
b = 129.189	β = 90
c = 165.115	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-25 
Deposition Author(s): Tan, K., Joachimiak, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2014-06-25
  Type: Initial release
  
• Version 1.1: 2015-04-29
  Changes: Non-polymer description
• Version 1.2: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary