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

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Basic information

Entry
Database: PDB / ID: 3imo
TitleStructure from the mobile metagenome of Vibrio cholerae. Integron cassette protein VCH_CASS14
ComponentsIntegron cassette protein
KeywordsUNKNOWN FUNCTION / Novel / Integron protein / Vibrio cholerae / Argentinean O139 strain
Function / homologyMetal Transport, Frataxin; Chain A - #70 / Integron cassette protein VCH_CASS1 chain / Integron cassette protein VCH_CASS1 chain / Metal Transport, Frataxin; Chain A / 2-Layer Sandwich / Alpha Beta / ACETATE ION / Integron cassette protein VCH-CASS1 chain domain-containing protein
Function and homology information
Biological speciesVibrio cholerae O139 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDeshpande, C.N. / Sureshan, V. / Harrop, S.J. / Boucher, Y. / Stokes, H.W. / Curmi, P.M.G. / Mabbutt, B.C.
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.G. / Mabbutt, B.C.
History
DepositionAug 11, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 6, 2013Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0896
Polymers58,9714
Non-polymers1182
Water3,747208
1
A: Integron cassette protein
C: Integron cassette protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5443
Polymers29,4852
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-18 kcal/mol
Surface area10870 Å2
MethodPISA
2
B: Integron cassette protein
D: Integron cassette protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5443
Polymers29,4852
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-17 kcal/mol
Surface area10710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.899, 64.705, 81.853
Angle α, β, γ (deg.)90.00, 131.26, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Integron cassette protein


Mass: 14742.679 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O139 (bacteria) / Strain: Arg3 O139 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: C7U313*PLUS
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsBOUND LIGANDS INCLUDE ACETATE ION FROM CRYSTALLIZATION SOLUTION AND A YET TO BE IDENTIFIED MOLECULE
Sequence detailsTHERE IS NO UNP REFERENCE SEQUENCE DATABASE FOR THIS PROTEIN AT THE TIME OF PROCESSING. THE FIRST ...THERE IS NO UNP REFERENCE SEQUENCE DATABASE FOR THIS PROTEIN AT THE TIME OF PROCESSING. THE FIRST 20 RESIDUES MGSSHHHHHHSSGLVPRGSH ARE EXPRESSION TAGS.

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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: 2.02 Å3/Da / Density % sol: 39.22 %
Crystal growTemperature: 296 K / Method: vapor diffusion
Details: 20% PEG 3350, 0.20M Lithium acetate, Cryoprotectant: Perfluoropolyether PFO-X175/08 (Hampton Research), VAPOR DIFFUSION, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03319 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 2, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 1.8→45.08 Å / Num. all: 43702 / Num. obs: 43702 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 30.693 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.077 / Net I/σ(I): 12.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 1.8 / Num. unique all: 6365 / Rsym value: 0.737 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX(phenix.autosol)model building
PHENIX(phenix.refine: 1.4_118)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: local model built from low resolution SAD data from p212121 selenomethionine crystals

Resolution: 1.8→32.568 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.26 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.22 / Phase error: 26.02 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2296 4294 5.03 %RANDOM
Rwork0.1934 81121 --
all0.1953 85415 --
obs0.1953 41948 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.035 Å2 / ksol: 0.391 e/Å3
Displacement parametersBiso max: 164.07 Å2 / Biso mean: 45.852 Å2 / Biso min: 17.81 Å2
Baniso -1Baniso -2Baniso -3
1-6.133 Å20 Å27.374 Å2
2---0.548 Å2-0 Å2
3----5.585 Å2
Refinement stepCycle: LAST / Resolution: 1.8→32.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3435 0 8 208 3651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073498
X-RAY DIFFRACTIONf_angle_d0.9444718
X-RAY DIFFRACTIONf_chiral_restr0.059536
X-RAY DIFFRACTIONf_plane_restr0.003601
X-RAY DIFFRACTIONf_dihedral_angle_d14.0241250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.38241460.37112657X-RAY DIFFRACTION99
1.8205-1.84190.31181520.32692725X-RAY DIFFRACTION100
1.8419-1.86430.34511460.30882681X-RAY DIFFRACTION99
1.8643-1.88790.36811420.29652717X-RAY DIFFRACTION100
1.8879-1.91280.28631480.28282661X-RAY DIFFRACTION100
1.9128-1.9390.32581290.26282791X-RAY DIFFRACTION100
1.939-1.96670.26521380.25432639X-RAY DIFFRACTION99
1.9667-1.9960.34151190.24292773X-RAY DIFFRACTION100
1.996-2.02720.31281690.24562614X-RAY DIFFRACTION100
2.0272-2.06050.27241330.23372760X-RAY DIFFRACTION100
2.0605-2.0960.29441490.20932675X-RAY DIFFRACTION99
2.096-2.13410.22851520.20272701X-RAY DIFFRACTION100
2.1341-2.17510.23291330.18952721X-RAY DIFFRACTION100
2.1751-2.21950.22991420.18272711X-RAY DIFFRACTION100
2.2195-2.26780.22371330.17772747X-RAY DIFFRACTION100
2.2678-2.32050.21331120.17212749X-RAY DIFFRACTION100
2.3205-2.37850.2581490.17982622X-RAY DIFFRACTION100
2.3785-2.44280.22381510.17582726X-RAY DIFFRACTION100
2.4428-2.51470.23471640.17742714X-RAY DIFFRACTION100
2.5147-2.59580.23391510.17912678X-RAY DIFFRACTION100
2.5958-2.68850.22821550.1722697X-RAY DIFFRACTION100
2.6885-2.79610.21061450.16612727X-RAY DIFFRACTION100
2.7961-2.92330.22331470.19062728X-RAY DIFFRACTION100
2.9233-3.07730.23721200.19632718X-RAY DIFFRACTION100
3.0773-3.26990.25631560.19882705X-RAY DIFFRACTION100
3.2699-3.52210.23481230.18782694X-RAY DIFFRACTION100
3.5221-3.87610.22331600.17262704X-RAY DIFFRACTION100
3.8761-4.43570.15511200.15272751X-RAY DIFFRACTION100
4.4357-5.5840.17981670.1552682X-RAY DIFFRACTION100
5.584-32.57350.22391430.20592653X-RAY DIFFRACTION97
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)
10.7151-0.3540.46132.541-0.23093.0302-0.060.01850.0917-0.1929-0.0159-0.05380.22880.12670.07070.1850.02270.00070.18110.01240.212310.3128-10.67923.5442
20.98130.1964-1.33790.8945-0.24394.8038-0.0067-0.0187-0.06110.22740.01430.082-0.27230.019-0.00610.2511-0.00830.02730.1605-0.02590.229931.7189-37.437717.4178
32.7105-0.19360.00512.70981.53152.5572-0.2569-0.4198-0.06491.06320.2092-0.08240.3626-0.08050.02750.43530.0888-0.05860.2489-0.02170.16519.7701-6.540744.7526
42.62070.141-2.59820.3929-0.23834.82440.16770.25310.0116-0.2323-0.0122-0.0483-0.49820.2076-0.16160.3172-0.05760.03850.2982-0.03980.250940.1266-33.8522-1.1682
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA0 - 113
2X-RAY DIFFRACTION2chain BB0 - 113
3X-RAY DIFFRACTION3chain CC2 - 113
4X-RAY DIFFRACTION4chain DD2 - 113

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