4L8K | pdb_00004l8k

Crystal structure of a putative peptidase (PARMER_02772) from Parabacteroides merdae ATCC 43184 at 2.26 A resolution

PDB DOI: https://doi.org/10.2210/pdb4L8K/pdb

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

Deposited: 2013-06-17 Released: 2013-07-03
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free:
0.206 (Depositor), 0.212 (DCC)
R-Value Work:
0.159 (Depositor), 0.164 (DCC)
R-Value Observed:
0.162 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4L8K

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of a putative peptidase (PARMER_02772) from Parabacteroides merdae ATCC 43184 at 2.26 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 150.08 kDa
Atom Count: 10,840
Modeled Residue Count: 1,246
Deposited Residue Count: 1,280
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative peptidase	A, B, C, D	320	Parabacteroides merdae ATCC 43184	Mutation(s): 0 Gene Names: PARMER_02772, ZP_02032754.1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MRD Query on MRD Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] MOL2 format, chain M [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] mmCIF format, chain M [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C]	M [auth B], R [auth C], S [auth C]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C] Interactions & Density Focus chain M [auth B] Focus chain R [auth C] Focus chain S [auth C]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain Q [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D]	F [auth A] G [auth A] K [auth B] L [auth B] Q [auth C] F [auth A], G [auth A], K [auth B], L [auth B], Q [auth C], W [auth D], X [auth D]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain Q [auth C] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain Q [auth C] Focus chain W [auth D] Focus chain X [auth D]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D]	E [auth A] I [auth B] J [auth B] N [auth C] O [auth C] E [auth A], I [auth B], J [auth B], N [auth C], O [auth C], P [auth C], U [auth D], V [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain U [auth D] Focus chain V [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain T [auth C] MOL2 format, chain H [auth A] MOL2 format, chain T [auth C] mmCIF format, chain H [auth A] mmCIF format, chain T [auth C]	H [auth A], T [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain T [auth C] Interactions & Density Focus chain H [auth A] Focus chain T [auth C]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.26 Å
R-Value Free: 0.206 (Depositor), 0.212 (DCC)
R-Value Work: 0.159 (Depositor), 0.164 (DCC)
R-Value Observed: 0.162 (Depositor)

Diffraction Data:

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.333	α = 90
b = 131.213	β = 90.55
c = 129.056	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
PDB_EXTRACT	data extraction
SOLVE	phasing
XSCALE	data scaling
BUSTER-TNT	refinement
XDS	data reduction
BUSTER	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-07-03

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2013-07-03
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-02-01
Changes: Database references, Derived calculations
Version 1.4: 2024-10-09
Changes: Data collection, Structure summary

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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.