4S1P | pdb_00004s1p

Shel_16390 protein, a putative SGNH hydrolase from Slackia heliotrinireducens

PDB DOI: https://doi.org/10.2210/pdb4S1P/pdb

Classification: HYDROLASE
Organism(s): Slackia heliotrinireducens DSM 20476
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-01-14 Released: 2015-01-28
Deposition Author(s): Osipiuk, J., Cuff, M.E., Wu, R., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.156 (Depositor), 0.169 (DCC)
R-Value Work:
0.118 (Depositor), 0.133 (DCC)
R-Value Observed:
0.119 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 4S1P

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

Literature

Shel_16390 protein, a putative SGNH hydrolase from Slackia heliotrinireducens

Osipiuk, J., Cuff, M.E., Wu, R., Endres, M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 20.42 kDa
Atom Count: 1,646
Modeled Residue Count: 184
Deposited Residue Count: 191
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A	191	Slackia heliotrinireducens DSM 20476	Mutation(s): 0 Gene Names: Shel_16390
UniProt
Find proteins for C7N6X3 (Slackia heliotrinireducens (strain ATCC 29202 / DSM 20476 / NCTC 11029 / RHS 1)) Explore C7N6X3 Go to UniProtKB: C7N6X3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C7N6X3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UNL Query on UNL Download:Ideal Coordinates CCD File	B [auth A]	Unknown ligand		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.156 (Depositor), 0.169 (DCC)
R-Value Work: 0.118 (Depositor), 0.133 (DCC)
R-Value Observed: 0.119 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.591	α = 90
b = 67.023	β = 90
c = 71.544	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SHELXCD	phasing
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-01-28

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2015-01-28
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2024-10-16
Changes: Data collection, Database references, Derived calculations, 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.