7V52 | pdb_00007v52

Structure of AdaV

PDB DOI: https://doi.org/10.2210/pdb7V52/pdb

Classification: OXIDOREDUCTASE
Organism(s): Actinomadura sp. ATCC 39365
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2021-08-16 Released: 2022-08-24
Deposition Author(s): Zhang, Z.Y., Chen, W.Q., Zhai, G.Q., Zhang, M.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.38 Å
R-Value Free:
0.213 (Depositor), 0.220 (DCC)
R-Value Work:
0.201 (Depositor), 0.210 (DCC)
R-Value Observed:
0.202 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Structural Insight into the Catalytic Mechanism of Non-Heme Iron Halogenase AdaV in 2'-Chloropentostatin Biosynthesis

Zhai, G.Q., Gong, R., Lin, Y., Zhang, M., Li, J., Deng, Z., Sun, J., Chen, W., Zhang, Z.G.

(2022) ACS Catal 12: 13910-13920

DOI: https://doi.org/10.1021/acscatal.2c04608

Macromolecule Content

Total Structure Weight: 36.08 kDa
Atom Count: 2,131
Modeled Residue Count: 267
Deposited Residue Count: 330
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AdaV	A	330	Actinomadura sp. ATCC 39365	Mutation(s): 1
UniProt
Find proteins for A0A1U8X168 (Actinomadura sp. ATCC 39365) Explore A0A1U8X168 Go to UniProtKB: A0A1U8X168
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1U8X168
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FE (Subject of Investigation/LOI) Query on FE 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]	FE (III) ION Fe VTLYFUHAOXGGBS-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: 2.38 Å
R-Value Free: 0.213 (Depositor), 0.220 (DCC)
R-Value Work: 0.201 (Depositor), 0.210 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.98	α = 90
b = 139.98	β = 90
c = 48.204	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
CRANK2	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-08-24

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	2018YFA0903200

Revision History (Full details and data files)

Version 1.0: 2022-08-24
Type: Initial release
Version 1.1: 2022-11-09
Changes: Structure summary
Version 1.2: 2023-03-01
Changes: Database references
Version 1.3: 2024-05-29
Changes: Data collection

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.