7V4O | pdb_00007v4o

Unique non-heme hydroxylase in biosynthesis of nucleoside antibiotic pathway uncover mechanism of reaction

PDB DOI: https://doi.org/10.2210/pdb7V4O/pdb

Classification: ANTIBIOTIC
Organism(s): Streptomyces sp. MK730-62F2
Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpGUT1
Mutation(s): Yes

Deposited: 2021-08-13 Released: 2022-02-23
Deposition Author(s): Li, T.L., Saeid, M.Z.
Funding Organization(s): Academia Sinica (Taiwan)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.214 (Depositor), 0.214 (DCC)
R-Value Work:
0.180 (Depositor), 0.180 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

beta-Hydroxylation of alpha-amino-beta-hydroxylbutanoyl-glycyluridine catalyzed by a nonheme hydroxylase ensures the maturation of caprazamycin

Zadeh, S.M., Chen, M.H., Wang, Z.C., Astani, E.K., Lo, I.W., Lin, K.H., Hsu, N.S., Adhikari, K., Lyu, S.Y., Tsai, H.Y., Terasawa, Y., Yabe, M., Yamamoto, K., Ichikawa, S., Li, T.L.

(2022) Commun Chem 5: 87

DOI: https://doi.org/10.1038/s42004-022-00703-6

Macromolecule Content

Total Structure Weight: 42.51 kDa
Atom Count: 3,337
Modeled Residue Count: 352
Deposited Residue Count: 364
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-hydroxylase	A [auth B], B [auth A]	182	Streptomyces sp. MK730-62F2	Mutation(s): 1 Gene Names: cpz10
UniProt
Find proteins for C4NCJ7 (Streptomyces sp. MK730-62F2) Explore C4NCJ7 Go to UniProtKB: C4NCJ7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C4NCJ7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
P3G Query on P3G Download:Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain D [auth A] MOL2 format, chain C [auth B] MOL2 format, chain D [auth A] mmCIF format, chain C [auth B] mmCIF format, chain D [auth A]	C [auth B], D [auth A]	3,6,9,12,15-PENTAOXAHEPTADECANE C₁₂ H₂₆ O₅ HYDWALOBQJFOMS-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Focus chain D [auth A] Interactions & Density Focus chain C [auth B] Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.214 (Depositor), 0.214 (DCC)
R-Value Work: 0.180 (Depositor), 0.180 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.839	α = 90
b = 39.035	β = 119.34
c = 76.591	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-02-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Academia Sinica (Taiwan)	Taiwan	108-2113-M-001-021-MY3

Revision History (Full details and data files)

Version 1.0: 2022-02-23
Type: Initial release
Version 1.1: 2022-08-10
Changes: Database references
Version 1.2: 2023-11-29
Changes: Data collection, Refinement description

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.