5BMT | pdb_00005bmt

Crystal structure of an uncharacterized protein (PARMER_03598) from Parabacteroides merdae ATCC 43184 at 1.50 A resolution

PDB DOI: https://doi.org/10.2210/pdb5BMT/pdb

Classification: UNKNOWN FUNCTION
Organism(s): Parabacteroides merdae ATCC 43184
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-05-23 Released: 2015-06-10
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.186 (Depositor), 0.190 (DCC)
R-Value Work:
0.166 (Depositor), 0.170 (DCC)
R-Value Observed:
0.167 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of an uncharacterized protein (PARMER_03598) from Parabacteroides merdae ATCC 43184 at 1.50 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 53.96 kDa
Atom Count: 4,577
Modeled Residue Count: 460
Deposited Residue Count: 478
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	239	Parabacteroides merdae ATCC 43184	Mutation(s): 0 Gene Names: PARMER_03598
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CXS Query on CXS Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B], K [auth B], L [auth B]	3-CYCLOHEXYL-1-PROPYLSULFONIC ACID C₉ H₁₉ N O₃ S PJWWRFATQTVXHA-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], I [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain I [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain M [auth B] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], M [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain M [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain H [auth A] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain H [auth A] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain H [auth A]	H [auth A], N [auth B], O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain H [auth A] Focus chain N [auth B] Focus chain O [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.186 (Depositor), 0.190 (DCC)
R-Value Work: 0.166 (Depositor), 0.170 (DCC)
R-Value Observed: 0.167 (Depositor)

Diffraction Data: https://doi.org/10.18430/M3SW2S

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.75	α = 90
b = 58.969	β = 90
c = 165.462	γ = 90

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
SHELX	phasing
SHARP	phasing
XDS	data reduction
XSCALE	data scaling
BUSTER	refinement
SHELXD	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-06-10

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2015-06-10
Type: Initial release
Version 1.1: 2018-01-24
Changes: Database references, Derived calculations, Source and taxonomy
Version 1.2: 2023-02-01
Changes: Database references
Version 1.3: 2024-10-23
Changes: Data collection, Structure summary