3K89 | pdb_00003k89

Structure of X. oryzae pv. oryzae KACC10331, Xoo0880(fabD) complexed with glycerol

• PDB DOI: https://doi.org/10.2210/pdb3K89/pdb

• Classification: TRANSFERASE
• Organism(s): Xanthomonas oryzae pv. oryzae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-10-14 Released: 2009-10-27 
• Deposition Author(s): Natarajan, S., Jung, J.W., Kang, L.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Structure of X. oryzae pv. oryzae KACC10331, Xoo0880(fabD) complexed with glycerol

Natarajan, S., Jung, J.W., Kang, L.W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 32.74 kDa 
• Atom Count: 2,699 
• Modeled Residue Count: 314 
• Deposited Residue Count: 314 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Malonyl CoA-ACP transacylase	A	314	Xanthomonas oryzae pv. oryzae	Mutation(s): 0  Gene Names: fabD, XOO0880 EC: 2.3.1.39
UniProt
Find proteins for Q5H4I7 (Xanthomonas oryzae pv. oryzae (strain KACC10331 / KXO85)) Explore Q5H4I7  Go to UniProtKB:  Q5H4I7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.361	α = 90
b = 74.095	β = 90
c = 98.617	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-27 
Deposition Author(s): Natarajan, S., Jung, J.W., Kang, L.W.

Revision History  

• Version 1.0: 2009-10-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description