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- PDB-3gk6: Crystal structure from the mobile metagenome of Vibrio cholerae. ... -

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Basic information

Entry
Database: PDB / ID: 3gk6
TitleCrystal structure from the mobile metagenome of Vibrio cholerae. Integron cassette protein VCH_CASS2.
ComponentsIntegron cassette protein VCH_CASS2
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Novel / Integron cassette protein / Vibrio cholerae / Oyster pond / Woods hole / USA / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Integron-associated effector binding protein / Integron-associated effector binding protein / Bacterial transcription activator, effector binding / Bacterial transcription activator, effector binding domain / Multidrug-efflux Transporter 1 Regulator Bmrr; Chain A / Regulatory factor, effector binding domain / Regulatory factor, effector binding domain superfamily / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Integron cassette protein VCH_CASS2
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsDeshpande, C.N. / Sureshan, V. / Harrop, S.J. / Boucher, Y. / Xu, X. / Cui, H. / Edwards, A.M. / Savchenko, A. / Joachimiak, A. / Chang, C. ...Deshpande, C.N. / Sureshan, V. / Harrop, S.J. / Boucher, Y. / Xu, X. / Cui, H. / Edwards, A.M. / Savchenko, A. / Joachimiak, A. / Chang, C. / Stokes, H.W. / Curmi, P.M.G. / Mabbutt, B.C. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Plos One / Year: 2011
Title: Crystal Structure of an Integron Gene Cassette-Associated Protein from Vibrio cholerae Identifies a Cationic Drug-Binding Module.
Authors: Deshpande, C.N. / Harrop, S.J. / Boucher, Y. / Hassan, K.A. / Leo, R.D. / Xu, X. / Cui, H. / Savchenko, A. / Chang, C. / Labbate, M. / Paulsen, I.T. / Stokes, H.W. / Curmi, P.M. / Mabbutt, B.C.
History
DepositionMar 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integron cassette protein VCH_CASS2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8372
Polymers19,4831
Non-polymers3541
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.378, 59.378, 95.756
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Integron cassette protein VCH_CASS2


Mass: 19482.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: OPVCH_OP4G / Plasmid: p15TV-L / Production host: Escherichia coli (E. coli) / References: UniProt: D0VX23*PLUS
#2: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 / Polyethylene glycol


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.5 Å3/Da / Density % sol: 50.82 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 0.1M Citric acid, 25% PEG 3350, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97953 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97953 Å / Relative weight: 1
ReflectionResolution: 1.8→47.89 Å / Num. all: 34832 / Num. obs: 34832 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Biso Wilson estimate: 27.219 Å2 / Rmerge(I) obs: 0.062 / Rsym value: 0.079 / Net I/σ(I): 21
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 3.6 / Num. unique all: 2650 / Rsym value: 0.624 / % possible all: 99.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AutoSolphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→35.041 Å / SU ML: 0.27 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used in phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 1782 5.12 %RANDOM
Rwork0.1832 ---
all0.1852 34832 --
obs0.1852 34832 99.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.411 Å2 / ksol: 0.408 e/Å3
Refinement stepCycle: LAST / Resolution: 1.8→35.041 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1220 0 17 108 1345
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_bond_d_na1.047
X-RAY DIFFRACTIONf_bond_d_prot
X-RAY DIFFRACTIONf_angle_d
X-RAY DIFFRACTIONf_angle_d_na
X-RAY DIFFRACTIONf_angle_d_prot
X-RAY DIFFRACTIONf_angle_deg
X-RAY DIFFRACTIONf_angle_deg_na
X-RAY DIFFRACTIONf_angle_deg_prot
X-RAY DIFFRACTIONf_dihedral_angle_d
X-RAY DIFFRACTIONf_dihedral_angle_d_na
X-RAY DIFFRACTIONf_dihedral_angle_d_prot
X-RAY DIFFRACTIONf_improper_angle_d
X-RAY DIFFRACTIONf_improper_angle_d_na
X-RAY DIFFRACTIONf_improper_angle_d_prot
X-RAY DIFFRACTIONf_mcbond_it
X-RAY DIFFRACTIONf_mcangle_it
X-RAY DIFFRACTIONf_scbond_it
X-RAY DIFFRACTIONf_scangle_it
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 (%)
1.8-1.8490.30271730.27042512100
1.849-1.90340.24911540.23552520100
1.9034-1.96480.25241620.20882522100
1.9648-2.0350.241360.18682522100
2.035-2.11650.25181490.18332581100
2.1165-2.21280.20771180.17712573100
2.2128-2.32940.22531360.17382536100
2.3294-2.47530.25171420.1692557100
2.4753-2.66640.20381350.18232555100
2.6664-2.93460.22231300.1822576100
2.9346-3.3590.21781180.18812543100
3.359-4.23080.23891080.16492592100
4.2308-35.04780.19591210.1773246195
Refinement TLS params.Method: refined / Origin x: 15.3857 Å / Origin y: 29.826 Å / Origin z: 29.2665 Å
111213212223313233
T0.2452 Å20.064 Å20.0099 Å2-0.1324 Å20.0251 Å2--0.1737 Å2
L2.6536 °2-1.7463 °2-0.1047 °2-4.1546 °2-0.5796 °2--1.7721 °2
S0.1834 Å °0.0641 Å °0.1454 Å °-0.4936 Å °-0.1026 Å °-0.1499 Å °0.0036 Å °0.015 Å °-0.0743 Å °
Refinement TLS groupSelection details: chain A

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