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- PDB-3jrt: Structure from the mobile metagenome of V. paracholerae: Integron... -

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Basic information

Entry
Database: PDB / ID: 3jrt
TitleStructure from the mobile metagenome of V. paracholerae: Integron cassette protein Vpc_cass2
ComponentsIntegron cassette protein Vpc_cass2
KeywordsStructural Genomics / Unknown function / Integron cassette protein / Vibrio paracholerae / Mobile metagenome / PSI-2 Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyFour Helix Bundle (Hemerythrin (Met), subunit A) - #1060 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Function and homology information
Biological speciesVibrio paracholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsHarrop, S.J. / Deshpande, C. / Sureshan, V. / Boucher, Y. / Xu, X. / Cui, H. / Cuff, M. / Edwards, A. / Savchenko, A. / Joachimiak, A. ...Harrop, S.J. / Deshpande, C. / Sureshan, V. / Boucher, Y. / Xu, X. / Cui, H. / Cuff, M. / Edwards, A. / Savchenko, A. / Joachimiak, A. / 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
DepositionSep 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 6, 2013Group: Database references
Revision 1.3Nov 20, 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

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Assembly

Deposited unit
A: Integron cassette protein Vpc_cass2


Theoretical massNumber of molelcules
Total (without water)22,2821
Polymers22,2821
Non-polymers00
Water54030
1
A: Integron cassette protein Vpc_cass2

A: Integron cassette protein Vpc_cass2


Theoretical massNumber of molelcules
Total (without water)44,5642
Polymers44,5642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area3040 Å2
ΔGint-16 kcal/mol
Surface area16700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.510, 85.510, 46.656
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

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Components

#1: Protein Integron cassette protein Vpc_cass2


Mass: 22282.029 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio paracholerae (bacteria) / Plasmid: p15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.34 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 20% PEG3350, 0.2 M disodium tartrate. In situ proteolysis with chymotrypsin, pH 7.3, 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: 0.97929 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 25, 2008
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.3→29.003 Å / Num. all: 8801 / Num. obs: 8801 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Biso Wilson estimate: 48.3 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 21.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 1.6 / Num. measured all: 18536 / Num. unique all: 1281 / Rsym value: 0.473 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data processing
PHENIX1.4_151refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→27.99 Å / Occupancy max: 1 / Occupancy min: 0.48 / SU ML: 0.31 / Isotropic thermal model: TLS and individual isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 22.09 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.234 871 9.92 %random
Rwork0.189 ---
all0.193 8782 --
obs0.193 8782 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.884 Å2 / ksol: 0.305 e/Å3
Displacement parametersBiso max: 396.66 Å2 / Biso mean: 66.901 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1--5.371 Å20 Å20 Å2
2---5.371 Å2-0 Å2
3---10.742 Å2
Refinement stepCycle: LAST / Resolution: 2.3→27.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1337 0 0 30 1367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081369
X-RAY DIFFRACTIONf_angle_d0.9681847
X-RAY DIFFRACTIONf_chiral_restr0.075207
X-RAY DIFFRACTIONf_plane_restr0.004235
X-RAY DIFFRACTIONf_dihedral_angle_d15.416511
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3-2.4440.2351440.19513111455
2.444-2.6330.2611440.20713131457
2.633-2.8980.2531480.19812921440
2.898-3.3160.2441470.21113151462
3.316-4.1760.2551390.17613261465
4.176-27.9920.1971490.17213541503
Refinement TLS params.Method: refined / Origin x: 14.2965 Å / Origin y: 29.3796 Å / Origin z: 15.5965 Å
111213212223313233
T-0.1133 Å20.0422 Å2-0.072 Å2-0.2441 Å2-0.0851 Å2--0.1122 Å2
L3.2536 °2-0.258 °2-0.7732 °2-5.3413 °20.8459 °2--4.3897 °2
S0.119 Å °0.6913 Å °-0.2238 Å °0.0881 Å °-0.1323 Å °0.5678 Å °0.2805 Å °-0.4891 Å °0.0267 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 169
2X-RAY DIFFRACTION1allA1 - 201

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