2HYB | pdb_00002hyb

Crystal Structure of Hexameric DsrEFH

PDB DOI: https://doi.org/10.2210/pdb2HYB/pdb

Classification: TRANSFERASE
Organism(s): Allochromatium vinosum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2006-08-04 Released: 2007-07-03
Deposition Author(s): Shin, D.H., Connie, H., Schulte, A., Dahl, C., Kim, R., Kim, S.H., Berkeley Structural Genomics Center (BSGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.262 (Depositor), 0.261 (DCC)
R-Value Work:
0.206 (Depositor), 0.205 (DCC)
R-Value Observed:
0.206 (Depositor)

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

Literature

Crystal structure of hexameric DsrEFH

Shin, D.H., Connie, H., Schulte, A., Dahl, C., Kim, R., Kim, S.H.

To be published.

Macromolecule Content

Total Structure Weight: 247.85 kDa
Atom Count: 17,611
Modeled Residue Count: 2,178
Deposited Residue Count: 2,208
Unique protein chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative sulfurtransferase dsrE	A, D, G, J, M A, D, G, J, M, P	130	Allochromatium vinosum	Mutation(s): 0 Gene Names: dsrE EC: 2.8.1
UniProt
Find proteins for O87896 (Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D)) Explore O87896 Go to UniProtKB: O87896
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O87896
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Intracellular sulfur oxidation protein dsrF	B, E, H, K, N B, E, H, K, N, Q	136	Allochromatium vinosum	Mutation(s): 0 Gene Names: dsrF
UniProt
Find proteins for O87897 (Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D)) Explore O87897 Go to UniProtKB: O87897
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O87897
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DsrH	C, F, I, L, O C, F, I, L, O, R	102	Allochromatium vinosum	Mutation(s): 0 Gene Names: dsrH
UniProt
Find proteins for O87898 (Allochromatium vinosum) Explore O87898 Go to UniProtKB: O87898
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O87898
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.262 (Depositor), 0.261 (DCC)
R-Value Work: 0.206 (Depositor), 0.205 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.61	α = 90
b = 183.11	β = 99.57
c = 107.83	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-07-03

Deposition Author(s):

Berkeley Structural Genomics Center (BSGC)

Revision History (Full details and data files)

Version 1.0: 2007-07-03
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-21
Changes: Data collection, Database references

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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.