7S5N | pdb_00007s5n

Crystal Structure of a Putative uncharacterized protein from Mycobacterium marinum

PDB DOI: https://doi.org/10.2210/pdb7S5N/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Mycobacterium marinum M
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-09-10 Released: 2021-09-22
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.219 (Depositor), 0.235 (DCC)
R-Value Work:
0.184 (Depositor)
R-Value Observed:
0.185 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 7S5N

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of a Putative uncharacterized protein from Mycobacterium marinum

Abendroth, J., Dranow, D.M., Sankaran, B., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Macromolecule Content

Total Structure Weight: 103.66 kDa
Atom Count: 6,686
Modeled Residue Count: 750
Deposited Residue Count: 882
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MymaA.17060.a	A, B, C, D, E A, B, C, D, E, F	147	Mycobacterium marinum M	Mutation(s): 0 Gene Names: MMAR_1385
UniProt
Find proteins for B2HFJ9 (Mycobacterium marinum (strain ATCC BAA-535 / M)) Explore B2HFJ9 Go to UniProtKB: B2HFJ9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2HFJ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain N [auth C] SDF format, chain S [auth E] SDF format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain S [auth E] MOL2 format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain S [auth E] mmCIF format, chain K [auth B]	K [auth B], N [auth C], S [auth E]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain K [auth B] Focus chain N [auth C] Focus chain S [auth E] Interactions & Density Focus chain K [auth B] Focus chain N [auth C] Focus chain S [auth E]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain P [auth D] SDF format, chain R [auth E] SDF format, chain T [auth F] SDF format, chain U [auth F] SDF format, chain Q [auth E] SDF format, chain O [auth D] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] MOL2 format, chain R [auth E] MOL2 format, chain T [auth F] MOL2 format, chain U [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain O [auth D] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D] mmCIF format, chain R [auth E] mmCIF format, chain T [auth F] mmCIF format, chain U [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain O [auth D] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth B] J [auth B] L [auth C] G [auth A], H [auth A], I [auth B], J [auth B], L [auth C], M [auth C], O [auth D], P [auth D], Q [auth E], R [auth E], T [auth F], U [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth E] Focus chain T [auth F] Focus chain U [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth E] Focus chain T [auth F] Focus chain U [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.219 (Depositor), 0.235 (DCC)
R-Value Work: 0.184 (Depositor)
R-Value Observed: 0.185 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.69	α = 90
b = 87.6	β = 90
c = 185.83	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
PHENIX	model building
Coot	model building

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2021-09-22

Deposition Author(s):

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History (Full details and data files)

Version 1.0: 2021-09-22
Type: Initial release
Version 1.1: 2024-04-03
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.