4RSH

Structure of a putative lipolytic protein of G-D-S-L family from Desulfitobacterium hafniense DCB-2

PDB DOI: https://doi.org/10.2210/pdb4RSH/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Desulfitobacterium hafniense DCB-2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-11-07 Released: 2014-11-19
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: 2.19 Å
R-Value Free: 0.270
R-Value Work: 0.199
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

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

Literature

Structure of a putative lipolytic protein of G-D-S-L family from Desulfitobacterium hafniense DCB-2

Filippova, E.V., Wawrzak, Z., Minasov, G., Kiryukhina, O., Endres, M., Joachimiak, A., Anderson, W.F.

To be published.

Macromolecule Content

Total Structure Weight: 60.05 kDa
Atom Count: 4,429
Modelled Residue Count: 525
Deposited Residue Count: 537
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipolytic protein G-D-S-L family	A, B, C	179	Desulfitobacterium hafniense DCB-2	Mutation(s): 0 Gene Names: ACL22416, Dhaf_4411
UniProt
Find proteins for B8FVL4 (Desulfitobacterium hafniense (strain DSM 10664 / DCB-2)) Explore B8FVL4 Go to UniProtKB: B8FVL4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B8FVL4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain E [auth C] MOL2 format, chain D [auth B] MOL2 format, chain E [auth C] mmCIF format, chain D [auth B] mmCIF format, chain E [auth C]	D [auth B], E [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth B] Focus chain E [auth C]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.19 Å
R-Value Free: 0.270
R-Value Work: 0.199
R-Value Observed: 0.203
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.997	α = 90
b = 63.649	β = 90
c = 85.647	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2014-11-19

Deposition Author(s):

Filippova, E.V.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2014-11-19
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description

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.