3HB7 | pdb_00003hb7

The Crystal Structure of an Isochorismatase-like Hydrolase from Alkaliphilus metalliredigens to 2.3A

• PDB DOI: https://doi.org/10.2210/pdb3HB7/pdb

• Classification: HYDROLASE
• Organism(s): Alkaliphilus metalliredigens QYMF
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-05-04 Released: 2009-07-07 
• Deposition Author(s): Stein, A.J., Xu, X., Cui, H., Ng, J., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.238 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Literature

The Crystal Structure of an Isochorismatase-like Hydrolase from Alkaliphilus metalliredigens to 2.3A

Stein, A.J., Xu, X., Cui, H., Ng, J., Edwards, A., Savchenko, A., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 4-mer - A4 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 186.91 kDa 
• Atom Count: 11,682 
• Modeled Residue Count: 1,449 
• Deposited Residue Count: 1,632 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isochorismatase hydrolase	A, B [auth C], C [auth B], D, E, F, G, H	204	Alkaliphilus metalliredigens QYMF	Mutation(s): 0  Gene Names: Amet_4583
UniProt
Find proteins for A6TWT6 (Alkaliphilus metalliredigens (strain QYMF)) Explore A6TWT6  Go to UniProtKB:  A6TWT6

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	J [auth A], M [auth B], P [auth E], Q [auth F], R [auth G]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
NH4	I [auth A], K [auth C], L [auth B], N [auth D], O [auth E], S [auth H]	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.238 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.651	α = 90
b = 105.425	β = 103.9
c = 106.267	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	phasing
SHELX	phasing
MLPHARE	phasing
DM	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-07 
Deposition Author(s): Stein, A.J., Xu, X., Cui, H., Ng, J., Edwards, A., Savchenko, A., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2009-07-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary