4N9X | pdb_00004n9x

Crystal Structure of the OCTAPRENYL-METHYL-METHOXY-BENZQ MOLECULE from Erwina carotovora subsp. atroseptica strain SCRI 1043 / ATCC BAA-672, Northeast Structural Genomics Consortium (NESG) Target EwR161

PDB DOI: https://doi.org/10.2210/pdb4N9X/pdb

Classification: OXIDOREDUCTASE
Organism(s): Pectobacterium atrosepticum SCRI1043
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-10-21 Released: 2013-11-20
Deposition Author(s): Kuzin, A., Chen, Y., Lew, S., Seetharaman, J., Mao, L., Xiao, R., Owens, L.A., Wang, D., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.266 (Depositor), 0.263 (DCC)
R-Value Work:
0.225 (Depositor), 0.224 (DCC)
R-Value Observed:
0.227 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of the OCTAPRENYL-METHYL-METHOXY-BENZQ MOLECULE from Erwina carotovora subsp. atroseptica strain SCRI 1043 / ATCC BAA-672, Northeast Structural Genomics Consortium (NESG) Target EwR161

Kuzin, A., Chen, Y., Lew, S., Seetharaman, J., Mao, L., Xiao, R., Owens, L.A., Wang, D., Everett, J.K., Acton, T.B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

To be published.

Macromolecule Content

Total Structure Weight: 46.2 kDa
Atom Count: 2,902
Modeled Residue Count: 371
Deposited Residue Count: 411
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative monooxygenase	A	411	Pectobacterium atrosepticum SCRI1043	Mutation(s): 0 Gene Names: visC, ECA0457 EC: 1
UniProt
Find proteins for Q6DA06 (Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672)) Explore Q6DA06 Go to UniProtKB: Q6DA06
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6DA06
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	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: 0.266 (Depositor), 0.263 (DCC)
R-Value Work: 0.225 (Depositor), 0.224 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.098	α = 90
b = 120.098	β = 90
c = 149.924	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-11-20

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2013-11-20
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2023-12-06
Changes: Data collection
Version 1.3: 2024-11-06
Changes: Structure summary