3KKJ | pdb_00003kkj

X-ray structure of P. syringae q888a4 Oxidoreductase at resolution 2.5A, Northeast Structural Genomics Consortium target PsR10

PDB DOI: https://doi.org/10.2210/pdb3KKJ/pdb
Entry: 3KKJ supersedes: 1YVV

Classification: OXIDOREDUCTASE
Organism(s): Pseudomonas syringae pv. tomato
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-11-05 Released: 2009-11-24
Deposition Author(s): Kuzin, A.P., Chen, Y., Forouhar, F., Vorobiev, S., Acton, T., Ma, L.C., Xiao, R., Montelione, G.T., Hunt, J.F., Tong, T., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.281 (Depositor), 0.280 (DCC)
R-Value Work:
0.227 (Depositor), 0.227 (DCC)
R-Value Observed:
0.234 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

X-ray structure of P. syringae q888a4 Oxidoreductase at resolution 2.5A, Northeast Structural Genomics Consortium target PsR10

Kuzin, A.P., Chen, Y., Forouhar, F., Vorobiev, S., Acton, T., Ma, L.C., Xiao, R., Montelione, G.T., Hunt, J.F., Tong, T.

To be published.

Macromolecule Content

Total Structure Weight: 76.32 kDa
Atom Count: 5,328
Modeled Residue Count: 656
Deposited Residue Count: 672
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Amine oxidase, flavin-containing	A, B	336	Pseudomonas syringae pv. tomato	Mutation(s): 0 Gene Names: PSPTO1126, PSPTO_1126 EC: 1.6.3.5
UniProt
Find proteins for Q888A4 (Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000)) Explore Q888A4 Go to UniProtKB: Q888A4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q888A4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.281 (Depositor), 0.280 (DCC)
R-Value Work: 0.227 (Depositor), 0.227 (DCC)
R-Value Observed: 0.234 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.698	α = 90
b = 120.698	β = 90
c = 114.791	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
SOLVE	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-11-24

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

This entry supersedes: 1YVV

Revision History (Full details and data files)

Version 1.0: 2009-11-24
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2024-11-20
Changes: Data collection, Database references, Derived calculations, Structure summary