4RPC | pdb_00004rpc

Crystal structure of the putative alpha/beta hydrolase family protein from Desulfitobacterium hafniense

PDB DOI: https://doi.org/10.2210/pdb4RPC/pdb

Classification: HYDROLASE
Organism(s): Desulfitobacterium hafniense DCB-2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-10-30 Released: 2014-11-12
Deposition Author(s): Filippova, E.V., Wawrzak, Z., Minasov, G., Kiryukhina, O., Endres, M., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.247 (Depositor), 0.255 (DCC)
R-Value Work:
0.176 (Depositor), 0.190 (DCC)
R-Value Observed:
0.180 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the putative alpha/beta hydrolase family protein from Desulfitobacterium hafniense

Filippova, E.V., Wawrzak, Z., Minasov, G., Kiryukhina, O., Endres, M., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

To be published.

Macromolecule Content

Total Structure Weight: 60.14 kDa
Atom Count: 4,184
Modeled Residue Count: 500
Deposited Residue Count: 526
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative alpha/beta hydrolase	A, B	263	Desulfitobacterium hafniense DCB-2	Mutation(s): 0 Gene Names: Dhaf_3963
UniProt
Find proteins for B8FSW0 (Desulfitobacterium hafniense (strain DSM 10664 / DCB-2)) Explore B8FSW0 Go to UniProtKB: B8FSW0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8FSW0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
TRS Query on TRS Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

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: 2.10 Å
R-Value Free: 0.247 (Depositor), 0.255 (DCC)
R-Value Work: 0.176 (Depositor), 0.190 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.661	α = 90
b = 45.473	β = 90.56
c = 82.787	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-11-12

Deposition Author(s):

Filippova, E.V.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2014-11-12
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 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.