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- PDB-3g1j: Structure from the mobile metagenome of Vibrio cholerae. Integron... -

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Basic information

Entry
Database: PDB / ID: 3g1j
TitleStructure from the mobile metagenome of Vibrio cholerae. Integron cassette protein VCH_CASS4.
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 / homologymobile metagenome of vibrio cholerae. Integron cassette protein vch_cass4. / Domain of unknown function DUF3601 / Domain of unknown function (DUF3601) / SH3 type barrels. / Roll / Mainly Beta / Integron cassette protein
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 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: To be published
Title: Structure from the mobile metagenome of Vibrio cholerae. Integron cassette protein VCH_CASS4.
Authors: 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.
History
DepositionJan 30, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,2942
Polymers22,2942
Non-polymers00
Water3,945219
1
A: Integron cassette protein


Theoretical massNumber of molelcules
Total (without water)11,1471
Polymers11,1471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Integron cassette protein


Theoretical massNumber of molelcules
Total (without water)11,1471
Polymers11,1471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.043, 121.043, 27.014
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11B-122-

HOH

21B-228-

HOH

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Components

#1: Protein Integron cassette protein


Mass: 11147.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Plasmid: p15TV-L / Production host: Escherichia coli (E. coli) / References: UniProt: D0VX16*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST IN UNIPROT

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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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M Na(OAC), 0.2M NaFormate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97942 Å
DetectorType: SBC-3 / Detector: CCD / Date: Oct 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.7→24.668 Å / Num. all: 25217 / Num. obs: 25217 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 28.65 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 37.14
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1234 / Rsym value: 0.615 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIX(phenix.autosol)model building
PHENIX(phenix.refine)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→24.66 Å / Occupancy max: 1 / Occupancy min: 0.33 / SU ML: 0.24 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.05 / σ(I): 0 / Phase error: 21.65 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2189 1879 7.79 %RANDOM
Rwork0.1917 ---
all0.1938 24120 --
obs0.1938 24120 94.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.391 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso max: 133.6 Å2 / Biso min: 7.86 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→24.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1477 0 0 219 1696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071511
X-RAY DIFFRACTIONf_angle_d1.0232024
X-RAY DIFFRACTIONf_chiral_restr0.076199
X-RAY DIFFRACTIONf_plane_restr0.004266
X-RAY DIFFRACTIONf_dihedral_angle_d15.815556
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7003-1.74620.31051450.2707163792
1.7462-1.79760.28531380.2481169194
1.7976-1.85560.22951310.2348163193
1.8556-1.92190.32371420.2548168692
1.9219-1.99880.26931400.2251162192
1.9988-2.08970.24151400.2028171495
2.0897-2.19980.27361400.2035169094
2.1998-2.33760.23851440.2137172396
2.3376-2.51790.24511560.2044173697
2.5179-2.7710.22541540.2013178598
2.771-3.17120.21631500.1873179399
3.1712-3.99270.17741450.1457171493
3.9927-24.67080.17521540.1756182095
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
12.14620.22411.02190.48910.1651.0103-0.0668-0.00480.48360.0269-0.01040.11840.02820.10810.07720.080.01490.02440.13580.02520.16864.951954.511813.9454
20.99290.03910.2550.28870.06060.23720.00180.1990.28730.0496-0.01010.0330.00120.03040.01050.03920.08150.01790.160.06840.090331.819465.698312.7864
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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