3GJU | pdb_00003gju

Crystal structure of a putative aminotransferase (mll7127) from mesorhizobium loti maff303099 at 1.55 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3GJU/pdb

• Classification: TRANSFERASE
• Organism(s): Mesorhizobium japonicum MAFF 303099
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-03-09 Released: 2009-03-17 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.168 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.139 (Depositor), 0.149 (DCC) 
• R-Value Observed: 
  0.140 (Depositor) 

Literature

Crystal structure of putative aminotransferase (NP_107505.1) from Mesorhizobium loti at 1.55 A resolution

Joint Center for Structural Genomics (JCSG)

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: 50.94 kDa 
• Atom Count: 4,064 
• Modeled Residue Count: 459 
• Deposited Residue Count: 461 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative aminotransferase	A	460	Mesorhizobium japonicum MAFF 303099	Mutation(s): 1  Gene Names: mll7127, NP_107505.1
UniProt
Find proteins for Q987B2 (Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)) Explore Q987B2  Go to UniProtKB:  Q987B2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PLP	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
MPD	C [auth A], D [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
LLP	A	L-PEPTIDE LINKING	C14 H22 N3 O7 P		LYS
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.168 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.139 (Depositor), 0.149 (DCC) 
• R-Value Observed: 0.140 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33GJU

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.224	α = 90
b = 59.577	β = 130.59
c = 85.337	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-17 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-03-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations