3HZ7

Crystal Structure of the SirA-like protein (DSY4693) from Desulfitobacterium hafniense, Northeast Structural Genomics Consortium Target DhR2A

PDB DOI: https://doi.org/10.2210/pdb3HZ7/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Desulfitobacterium hafniense
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-06-23 Released: 2009-07-07
Deposition Author(s): Forouhar, F., Lew, S., Seetharaman, J., Sahdev, S., Xiao, R., Ciccosanti, C., Maglaqui, M., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.250 (Depositor), 0.261 (DCC)
R-Value Work:
0.228 (Depositor), 0.231 (DCC)
R-Value Observed:
0.229 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Northeast Structural Genomics Consortium Target DhR2A

Forouhar, F., Lew, S., Seetharaman, J., Sahdev, S., Xiao, R., Ciccosanti, C., Maglaqui, M., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Macromolecule Content

Total Structure Weight: 9.58 kDa
Atom Count: 590
Modelled Residue Count: 74
Deposited Residue Count: 87
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UPF0033 domain-containing protein	A	87	Desulfitobacterium hafniense	Mutation(s): 0 Gene Names: AT727_01915
UniProt
Find proteins for Q24NB0 (Desulfitobacterium hafniense (strain Y51)) Explore Q24NB0 Go to UniProtKB: Q24NB0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q24NB0
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSS Query on CSS	A	L-PEPTIDE LINKING	C₃ H₇ N O₂ S₂		CYS
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.250 (Depositor), 0.261 (DCC)
R-Value Work: 0.228 (Depositor), 0.231 (DCC)
R-Value Observed: 0.229 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.046	α = 90
b = 46.046	β = 90
c = 82.811	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
DENZO	data reduction
SCALEPACK	data scaling
SnB	phasing
REFMAC	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-07-07

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2009-07-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 2.0: 2024-11-20
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary