3RFC | pdb_00003rfc

Crystal structure of D-alanine-D-alanine ligase A from Xanthomonas oryzae pathovar oryzae with ADP

PDB DOI: https://doi.org/10.2210/pdb3RFC/pdb

Classification: LIGASE
Organism(s): Xanthomonas oryzae pv. oryzae MAFF 311018
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2011-04-06 Released: 2011-05-04
Deposition Author(s): Doan, T.T.N., Kim, J.K., Ahn, Y.J., Kang, L.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.282 (Depositor), 0.286 (DCC)
R-Value Work:
0.204 (Depositor), 0.213 (DCC)
R-Value Observed:
0.208 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Crystal structure of D-alanine-D-alanine ligase A from Xanthomonas oryzae pathovar oryzae with ADP

Doan, T.T.N., Kim, J.K., Ahn, Y.J., Kang, L.W.

To be published.

Macromolecule Content

Total Structure Weight: 42.21 kDa
Atom Count: 2,763
Modeled Residue Count: 344
Deposited Residue Count: 384
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-alanine--D-alanine ligase 1	A	384	Xanthomonas oryzae pv. oryzae MAFF 311018	Mutation(s): 1 EC: 6.3.2.4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP 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]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.282 (Depositor), 0.286 (DCC)
R-Value Work: 0.204 (Depositor), 0.213 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.236	α = 90
b = 83.236	β = 90
c = 98.277	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-05-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-05-04
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-03-20
Changes: Data collection, Database references, Derived calculations

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