5MLD | pdb_00005mld

Crystal Structure of RosB with bound intermediate AFP (8-demethyl-8-aminoriboflavin-5'-phosphate)

PDB DOI: https://doi.org/10.2210/pdb5MLD/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Streptomyces davaonensis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-12-06 Released: 2017-12-20
Deposition Author(s): Konjik, V., Bruenle, S., Demmer, U., Vanselow, A., Sandhoff, R., Mack, M., Ermler, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.213 (Depositor), 0.214 (DCC)
R-Value Work:
0.174 (Depositor), 0.175 (DCC)
R-Value Observed:
0.176 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

The crystal structure of RosB gives insights into the reaction mechanism of this first known member of a new family of flavodoxin-like enzymes

Konjik, V., Bruenle, S., Demmer, U., Vanselow, A., Sandhoff, R., Mack, M., Ermler, U.

To be published.

Macromolecule Content

Total Structure Weight: 234.85 kDa
Atom Count: 18,138
Modeled Residue Count: 2,016
Deposited Residue Count: 2,056
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BRAMP domain protein	A, B, C, D, E A, B, C, D, E, F, G, H	257	Streptomyces davaonensis	Mutation(s): 0 Gene Names: BN159_7989 EC: 2.6.1.114
UniProt
Find proteins for K4REZ6 (Streptomyces davaonensis (strain DSM 101723 / JCM 4913 / KCC S-0913 / 768)) Explore K4REZ6 Go to UniProtKB: K4REZ6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	K4REZ6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8DP Query on 8DP Download:Ideal Coordinates CCD File SDF format, chain P [auth H] SDF format, chain O [auth G] SDF format, chain N [auth F] SDF format, chain M [auth E] SDF format, chain L [auth D] SDF format, chain K [auth C] SDF format, chain J [auth B] SDF format, chain I [auth A] MOL2 format, chain P [auth H] MOL2 format, chain O [auth G] MOL2 format, chain N [auth F] MOL2 format, chain M [auth E] MOL2 format, chain L [auth D] MOL2 format, chain K [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] mmCIF format, chain P [auth H] mmCIF format, chain O [auth G] mmCIF format, chain N [auth F] mmCIF format, chain M [auth E] mmCIF format, chain L [auth D] mmCIF format, chain K [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A]	I [auth A] J [auth B] K [auth C] L [auth D] M [auth E] I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	8-demethyl-8-aminoriboflavin-5'-phosphate C₁₆ H₁₉ N₅ O₉ P SDTLZDHOYFRAPQ-WCQYABFASA-O		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.213 (Depositor), 0.214 (DCC)
R-Value Work: 0.174 (Depositor), 0.175 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.49	α = 90
b = 71.13	β = 92.08
c = 214.8	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2017-12-20

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-12-20
Type: Initial release
Version 1.1: 2019-10-16
Changes: Data collection
Version 1.2: 2024-05-08
Changes: Data collection, Database references

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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.