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- PDB-3fy6: Structure from the mobile metagenome of V. Cholerae. Integron cas... -

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Basic information

Entry
Database: PDB / ID: 3fy6
TitleStructure from the mobile metagenome of V. Cholerae. Integron cassette protein VCH_CASS3
ComponentsIntegron cassette protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Novel / Integron cassette protein / Vibrio cholerae / Oyster pond / Woodshole / USA / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyIntegron cassette protein fold / Integron cassette protein superfamily / : / : / Integron cassette protein / 2-Layer Sandwich / Alpha Beta / Integron cassette protein
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsDeshpande, C.N. / Sureshan, V. / Harrop, S.J. / Boucher, Y. / Xu, X. / Cui, H. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Tan, K. ...Deshpande, C.N. / Sureshan, V. / Harrop, S.J. / Boucher, Y. / Xu, X. / Cui, H. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Tan, K. / 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 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 27, 2013Group: Database references
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integron cassette protein
B: Integron cassette protein
C: Integron cassette protein
D: Integron cassette protein


Theoretical massNumber of molelcules
Total (without water)61,3014
Polymers61,3014
Non-polymers00
Water5,819323
1
A: Integron cassette protein
C: Integron cassette protein


Theoretical massNumber of molelcules
Total (without water)30,6512
Polymers30,6512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-25 kcal/mol
Surface area12110 Å2
MethodPISA
2
B: Integron cassette protein
D: Integron cassette protein


Theoretical massNumber of molelcules
Total (without water)30,6512
Polymers30,6512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-24 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.332, 97.398, 115.391
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Integron cassette protein


Mass: 15325.311 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: OPVCH_OP8A / Plasmid: p15TV-L / Production host: Escherichia coli (E. coli) / References: UniProt: M1E1E6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growMethod: vapor diffusion / pH: 4.6
Details: 0.1M sodium acetate , 2.0M sodium Formate, pH 4.6, VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.1→74.43 Å / Num. all: 33584 / Num. obs: 33584 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 24.992 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.13 / Net I/σ(I): 9.4
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 3 / Rsym value: 0.508 / % possible all: 99.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(phenix.autosol)model building
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→44.867 Å / SU ML: 0.26 / Isotropic thermal model: Isotropic / σ(F): 0.94 / Phase error: 20.65 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2238 2000 5.96 %
Rwork0.1695 --
obs0.1728 33541 98.98 %
all-33541 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.126 Å2 / ksol: 0.389 e/Å3
Refinement stepCycle: LAST / Resolution: 2.1→44.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4064 0 0 323 4387
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064178
X-RAY DIFFRACTIONf_angle_d0.945692
X-RAY DIFFRACTIONf_dihedral_angle_d16.8361504
X-RAY DIFFRACTIONf_chiral_restr0.064588
X-RAY DIFFRACTIONf_plane_restr0.004739
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15260.27861390.20572194X-RAY DIFFRACTION99
2.1526-2.21080.27691420.19592236X-RAY DIFFRACTION99
2.2108-2.27580.25681400.19112225X-RAY DIFFRACTION99
2.2758-2.34930.24711410.17842200X-RAY DIFFRACTION99
2.3493-2.43330.24111420.18182254X-RAY DIFFRACTION99
2.4333-2.53070.25341410.17542231X-RAY DIFFRACTION100
2.5307-2.64580.24881440.18272259X-RAY DIFFRACTION100
2.6458-2.78530.25461440.17082256X-RAY DIFFRACTION100
2.7853-2.95980.19241430.16642272X-RAY DIFFRACTION100
2.9598-3.18830.22151430.16772252X-RAY DIFFRACTION99
3.1883-3.5090.22261420.15812246X-RAY DIFFRACTION99
3.509-4.01650.18721450.14412274X-RAY DIFFRACTION98
4.0165-5.05920.18971440.14262278X-RAY DIFFRACTION98
5.0592-44.87720.21641500.18032364X-RAY DIFFRACTION97
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1refined0.8627-0.0761-0.2870.26180.01860.3188-0.0477-0.0759-0.18490.02380.04710.016-0.08790.00990.00210.10980.0224-0.00540.08220.00940.1002-5.985258.757742.9257
20.38280.1197-0.17890.32770.29820.45980.08110.14570.0157-0.0453-0.0467-0.1612-0.13090.0346-0.02890.1292-0.0023-0.0080.1248-0.01340.103
30.9594-0.2849-0.12260.22580.08790.1771-0.0159-0.0452-0.05450.00090.0553-0.0704-0.05010.0413-0.02840.1167-0.0106-0.00480.1161-0.01180.1795
40.73940.05650.15670.305-0.13540.28830.02610.24560.00070.05860.04080.0724-0.0041-0.0561-0.04750.11020.0148-0.0080.2226-0.00470.1251
Refinement TLS groupSelection details: chain D

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