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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.210 (Depositor), 0.194 (DCC)
R-Value Work:
0.179 (Depositor)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3K89

This is version 1.2 of the entry. See complete history.

Literature

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

Natarajan, S., Jung, J.W., Kang, L.W.

To be published.

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

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5H4I7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.210 (Depositor), 0.194 (DCC)
R-Value Work: 0.179 (Depositor)
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

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Entry History

Deposition Data

Released Date: 2009-10-27

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.