3HMU | pdb_00003hmu

Crystal structure of a class III aminotransferase from Silicibacter pomeroyi

• PDB DOI: https://doi.org/10.2210/pdb3HMU/pdb

• Classification: TRANSFERASE
• Organism(s): Ruegeria pomeroyi
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-05-29 Released: 2009-07-14 
• Deposition Author(s): Toro, R., Bonanno, J.B., Ramagopal, U., Freeman, J., Bain, K.T., Miller, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.193 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

Literature

Crystal structure of a class III aminotransferase from Silicibacter pomeroyi

Toro, R., Bonanno, J.B., Ramagopal, U., Freeman, J., Bain, K.T., Miller, S., Sauder, J.M., Burley, S.K., Almo, S.C.

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: 103.89 kDa 
• Atom Count: 7,782 
• Modeled Residue Count: 924 
• Deposited Residue Count: 944 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminotransferase, class III	A, B	472	Ruegeria pomeroyi	Mutation(s): 0  Gene Names: SPO3471
UniProt
Find proteins for Q5LMU1 (Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)) Explore Q5LMU1  Go to UniProtKB:  Q5LMU1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	D [auth A], F [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.193 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.246	α = 90
b = 113.605	β = 90
c = 130.985	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-07-14 
Deposition Author(s): Toro, R., Bonanno, J.B., Ramagopal, U., Freeman, J., Bain, K.T., Miller, S., Sauder, J.M., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2009-07-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.4: 2018-11-28
  Changes: Data collection, Source and taxonomy
• Version 1.5: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary
• Version 1.6: 2024-02-21
  Changes: Data collection, Database references