8S7M | pdb_00008s7m

RosC(R33A) - riboflavin complex

PDB DOI: https://doi.org/10.2210/pdb8S7M/pdb

Classification: HYDROLASE
Organism(s): Streptomyces davaonensis JCM 4913
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2024-03-04 Released: 2025-03-19
Deposition Author(s): Ermler, U., Mack, M., Warkentin, E.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.208 (Depositor), 0.208 (DCC)
R-Value Work:
0.178 (Depositor), 0.178 (DCC)
R-Value Observed:
0.179 (Depositor)

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Ligand Structure Quality Assessment

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Literature

Structural and kinetic analysis of phosphatase RosC, an enzyme of the biosynthesis of antibiotic roseoflavin

Joshi, T., Schneider, C., Glaser, T., Demmer, U., Warkentin, E., Ermler, U., Mack, M.

To be published.

Macromolecule Content

Total Structure Weight: 103.17 kDa
Atom Count: 7,488
Modeled Residue Count: 900
Deposited Residue Count: 936
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoglycerate mutase	A, B, C, D	234	Streptomyces davaonensis JCM 4913	Mutation(s): 1 Gene Names: BN159_8033
UniProt
Find proteins for K4R812 (Streptomyces davaonensis (strain DSM 101723 / JCM 4913 / KCC S-0913 / 768)) Explore K4R812 Go to UniProtKB: K4R812
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	K4R812
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RBF (Subject of Investigation/LOI) Query on RBF Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	RIBOFLAVIN C₁₇ H₂₀ N₄ O₆ AUNGANRZJHBGPY-SCRDCRAPSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain I [auth D] MOL2 format, chain I [auth D] mmCIF format, chain I [auth D]	I [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth D] Interactions & Density Focus chain I [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.208 (Depositor), 0.208 (DCC)
R-Value Work: 0.178 (Depositor), 0.178 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.86	α = 74.19
b = 51.99	β = 81.79
c = 81.43	γ = 70.77

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-03-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-03-19
Type: Initial release

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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.