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- PDB-3fxh: Crystal structure from the mobile metagenome of Halifax Harbour S... -

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Basic information

Entry
Database: PDB / ID: 3fxh
TitleCrystal structure from the mobile metagenome of Halifax Harbour Sewage Outfall: Integron Cassette Protein HFX_CASS2
ComponentsIntegron gene cassette protein HFX_CASS2
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Integron Cassette Protein / Mobile Metagenome / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyCrystal structure from the mobile metagenome of halifax harbour sewage outfall / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / Putative integron gene cassette protein
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.837 Å
AuthorsSureshan, V. / Deshpande, C. / Harrop, S.J. / Kudritska, M. / Koenig, J.E. / Evdokimova, E. / Chang, C. / Edwards, A.M. / Savchenko, A. / Joachimiak, A. ...Sureshan, V. / Deshpande, C. / Harrop, S.J. / Kudritska, M. / Koenig, J.E. / Evdokimova, E. / Chang, C. / 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)
CitationJournal: Plos One / Year: 2013
Title: Integron gene cassettes: a repository of novel protein folds with distinct interaction sites.
Authors: Sureshan, V. / Deshpande, C.N. / Boucher, Y. / Koenig, J.E. / Stokes, H.W. / Harrop, S.J. / Curmi, P.M. / Mabbutt, B.C.
History
DepositionJan 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 27, 2013Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Integron gene cassette protein HFX_CASS2


Theoretical massNumber of molelcules
Total (without water)15,5721
Polymers15,5721
Non-polymers00
Water1,72996
1
A: Integron gene cassette protein HFX_CASS2

A: Integron gene cassette protein HFX_CASS2


Theoretical massNumber of molelcules
Total (without water)31,1442
Polymers31,1442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area1810 Å2
ΔGint-10.8 kcal/mol
Surface area10810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.744, 66.829, 48.873
Angle α, β, γ (deg.)90.000, 113.520, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Integron gene cassette protein HFX_CASS2


Mass: 15571.861 Da / Num. of mol.: 1 / Fragment: UNP residues 10-114
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: ORF1 / Plasmid: p15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: B0BHE4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.21 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Tri-lithium citrate, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97923 Å
DetectorType: SBC-3 / Detector: CCD / Date: Oct 13, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.837→50 Å / Num. all: 10187 / Num. obs: 10187 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Χ2: 1.967 / Net I/σ(I): 35.289
Reflection shellResolution: 1.837→1.87 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 3.018 / Num. unique all: 252 / Rsym value: 0.669 / Χ2: 1.122 / % possible all: 95.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-3000data collection
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.837→26.787 Å / Occupancy max: 1 / Occupancy min: 0.66 / SU ML: 0.29 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1000 10.06 %random
Rwork0.186 ---
all0.191 9942 --
obs0.191 9942 94.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 79.651 Å2 / ksol: 0.376 e/Å3
Displacement parametersBiso max: 126.57 Å2 / Biso mean: 39.717 Å2 / Biso min: 16.87 Å2
Baniso -1Baniso -2Baniso -3
1--4.993 Å2-0 Å23.366 Å2
2---1.294 Å2-0 Å2
3---2.847 Å2
Refinement stepCycle: LAST / Resolution: 1.837→26.787 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms901 0 0 96 997
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007916
X-RAY DIFFRACTIONf_angle_d0.9241233
X-RAY DIFFRACTIONf_chiral_restr0.064140
X-RAY DIFFRACTIONf_plane_restr0.004159
X-RAY DIFFRACTIONf_dihedral_angle_d15.86333
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.837-1.9340.2971260.231167129386
1.934-2.0550.241460.1991257140394
2.055-2.2140.2221410.1771293143497
2.214-2.4370.2271480.181331147997
2.437-2.7890.2561510.1771290144196
2.789-3.5120.241440.181302144697
3.512-26.790.2331440.1851302144695
Refinement TLS params.Method: refined / Origin x: 26.4451 Å / Origin y: 43.0744 Å / Origin z: 8.8555 Å
111213212223313233
T0.2678 Å2-0.0047 Å2-0.0386 Å2-0.1794 Å20.0006 Å2--0.1567 Å2
L3.6891 °2-0.0069 °21.1684 °2-2.0454 °2-0.13 °2--5.624 °2
S0.0296 Å °-0.3332 Å °0.2585 Å °0.3347 Å °-0.2602 Å °-0.1729 Å °0.047 Å °0.3267 Å °0.1835 Å °
Refinement TLS groupSelection details: chain A

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