3GHJ | pdb_00003ghj

Crystal structure from the mobile metagenome of Halifax Harbour Sewage Outfall: Integron Cassette Protein HFX_CASS4

PDB DOI: https://doi.org/10.2210/pdb3GHJ/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): uncultured bacterium
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-03-03 Released: 2009-03-24
Deposition Author(s): Sureshan, V., Deshpande, C., Harrop, S.J., Kudritska, M., Koenig, J.E., Evdokimova, E., Kim, Y., Edwards, A.M., Savchenko, A., Joachimiak, A., Doolittle, W.F., Stokes, H.W., Curmi, P.M.G., Mabbutt, B.C., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free:
0.183 (Depositor), 0.180 (DCC)
R-Value Work:
0.168 (Depositor), 0.163 (DCC)
R-Value Observed:
0.169 (Depositor)

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This is version 1.4 of the entry. See complete history.

Literature

Structure from the mobile metagenome of Halifax Harbour Sewage Outfall: Integron Cassette Protein HFX_CASS4

Sureshan, V., Deshpande, C., Harrop, S.J., Kudritska, M., Koenig, J.E., Evdokimova, E., Kim, Y., Edwards, A.M., Savchenko, A., Joachimiak, A., Doolittle, W.F., Stokes, H.W., Curmi, P.M.G., Mabbutt, B.C.

To be published.

Macromolecule Content

Total Structure Weight: 16.33 kDa
Atom Count: 1,122
Modeled Residue Count: 116
Deposited Residue Count: 141
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative integron gene cassette protein	A	141	uncultured bacterium	Mutation(s): 1 Gene Names: ORF1
UniProt
Find proteins for A0ACD6B9H3 (uncultured bacterium) Explore A0ACD6B9H3 Go to UniProtKB: A0ACD6B9H3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0ACD6B9H3
Sequence Annotations Expand
Reference Sequence

Small Molecules

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: 1.47 Å
R-Value Free: 0.183 (Depositor), 0.180 (DCC)
R-Value Work: 0.168 (Depositor), 0.163 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.001	α = 90
b = 66.391	β = 90
c = 80.822	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-03-24

Deposition Author(s):

Doolittle, W.F.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-03-24
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: 2021-10-20
Changes: Database references, Derived calculations
Version 1.4: 2024-11-27
Changes: Data collection, 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.