4MM0 | pdb_00004mm0

Crystal Structure Analysis of the Putative Thioether Synthase SgvP Involved in the Tailoring Step of Griseoviridin

PDB DOI: https://doi.org/10.2210/pdb4MM0/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces griseoviridis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-09-07 Released: 2014-09-17
Deposition Author(s): Zhang, H., Huang, L., Yi, M., Cai, T., Zhang, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.214 (Depositor), 0.221 (DCC)
R-Value Work:
0.171 (Depositor), 0.181 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Structural Analysis of SgvP: a Putative Thioether Synthase Involved in the Tailoring Step of Griseoviridin

Zhang, H., Huang, L., Yi, M., Cai, T., Zhang, H.

To be published.

Macromolecule Content

Total Structure Weight: 89.04 kDa
Atom Count: 6,560
Modeled Residue Count: 786
Deposited Residue Count: 798
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
P450-like monooxygenase	A, B	399	Streptomyces griseoviridis	Mutation(s): 0 EC: 1.14.13
UniProt
Find proteins for R9USI6 (Streptomyces griseoviridis) Explore R9USI6 Go to UniProtKB: R9USI6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	R9USI6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.214 (Depositor), 0.221 (DCC)
R-Value Work: 0.171 (Depositor), 0.181 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 184.05	α = 90
b = 184.05	β = 90
c = 80.32	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-09-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-09-17
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, 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.