4X4J | pdb_00004x4j

Structural and Functional Studies of BexE: Insights into Oxidation During BE-7585A Biosynthesis

PDB DOI: https://doi.org/10.2210/pdb4X4J/pdb

Classification: OXIDOREDUCTASE
Organism(s): Amycolatopsis orientalis subsp. vinearia
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-12-02 Released: 2015-12-02
Deposition Author(s): Tsai, S.-C., Jackson, D.R., Patel, A., Barajas, J.F., Rohr, J., Yu, X., Liu, H.-W., Sasaki, E., Calveras, J., Metsa-Ketela, M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.246 (Depositor), 0.261 (DCC)
R-Value Work:
0.193 (Depositor)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural and Functional Studies of BexE: Insights into Oxidation During BE-7585A Biosynthesis

Tsai, S.-C., Jackson, D.R., Patel, A., Barajas, J.F., Rohr, J., Yu, X., Liu, H.-W., Sasaki, E., Calveras, J., Metsa-Ketela, M.

To be published.

Macromolecule Content

Total Structure Weight: 109.19 kDa
Atom Count: 7,341
Modeled Residue Count: 962
Deposited Residue Count: 1,014
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative oxygenase	A, B	507	Amycolatopsis orientalis subsp. vinearia	Mutation(s): 0 Gene Names: bexE
UniProt
Find proteins for D7RFJ3 (Amycolatopsis orientalis subsp. vinearia) Explore D7RFJ3 Go to UniProtKB: D7RFJ3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D7RFJ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	C [auth A], D [auth A], F [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.246 (Depositor), 0.261 (DCC)
R-Value Work: 0.193 (Depositor)
R-Value Observed: 0.197 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.672	α = 90
b = 80.379	β = 126.19
c = 105.079	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHASER	phasing
Coot	model building
HKL-2000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2015-12-02

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5R01GM100305-03

Revision History (Full details and data files)

Version 1.0: 2015-12-02
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence, Derived calculations, Refinement description
Version 1.2: 2019-12-25
Changes: Author supporting evidence
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Refinement description