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- PDB-3if4: Structure from the mobile metagenome of North West Arm Sewage Out... -

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Basic information

Entry
Database: PDB / ID: 3if4
TitleStructure from the mobile metagenome of North West Arm Sewage Outfall: Integron Cassette Protein Hfx_Cass5
ComponentsIntegron Cassette Protein Hfx_Cass5
Keywordsstructural genomics / unknown function / Integron Cassette Protein Mobile Metagenome Structural Genomics PSI-2 Protein Structure Initiative Midwest Center for Structural Genomics / MCSG
Function / homologyIntegron cassette protein helical domain / Integron cassette protein / Anthopleurin-A / Single Sheet / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Beta / Mainly Alpha
Function and homology information
Biological speciesunidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.181 Å
AuthorsSureshan, V. / Deshpande, C.N. / Harrop, S.J. / Evdokimova, E. / Kudrytska, M. / Koenig, J.E. / Osipiuk, J. / Edwards, A. / Savchenko, A. / Joachimiak, A. ...Sureshan, V. / Deshpande, C.N. / Harrop, S.J. / Evdokimova, E. / Kudrytska, M. / Koenig, J.E. / Osipiuk, J. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Doolittle, W.F. / 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
DepositionJul 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 6, 2013Group: Database references
Revision 1.3Oct 9, 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 / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integron Cassette Protein Hfx_Cass5
B: Integron Cassette Protein Hfx_Cass5
C: Integron Cassette Protein Hfx_Cass5
D: Integron Cassette Protein Hfx_Cass5


Theoretical massNumber of molelcules
Total (without water)54,5994
Polymers54,5994
Non-polymers00
Water2,360131
1
A: Integron Cassette Protein Hfx_Cass5
C: Integron Cassette Protein Hfx_Cass5


Theoretical massNumber of molelcules
Total (without water)27,2992
Polymers27,2992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-48 kcal/mol
Surface area11590 Å2
MethodPISA
2
B: Integron Cassette Protein Hfx_Cass5
D: Integron Cassette Protein Hfx_Cass5


Theoretical massNumber of molelcules
Total (without water)27,2992
Polymers27,2992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-48 kcal/mol
Surface area11770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.324, 44.481, 82.462
Angle α, β, γ (deg.)90.00, 109.81, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe four chains in the asymmetric unit arrange as two dimers. Dimer 1: Chain A and Chain C Dimer 2: Chain B and Chain D

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Components

#1: Protein
Integron Cassette Protein Hfx_Cass5


Mass: 13649.657 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: uncultured bacterium / Source: (gene. exp.) unidentified (others) / Plasmid: p15TV LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-CodonPlus(DE3)-RIPL
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 1.94 Å3/Da / Density % sol: 36.53 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 29% PEG3350, 0.1 M Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 5, 2009
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 21618 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 34.4 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 34.6
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 2.62 / Rsym value: 0.531 / % possible all: 68.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIX(phenix.autosol)model building
PHENIX(phenix.refine)refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.181→40.226 Å / SU ML: 0.3 / Isotropic thermal model: anisotropic / σ(F): 0.05 / Phase error: 24.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2328 1951 9.23 %
Rwork0.1777 --
obs0.1828 21127 95.41 %
all-21127 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.641 Å2 / ksol: 0.359 e/Å3
Refinement stepCycle: LAST / Resolution: 2.181→40.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3175 0 0 131 3306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053318
X-RAY DIFFRACTIONf_angle_d0.8764531
X-RAY DIFFRACTIONf_dihedral_angle_d17.141191
X-RAY DIFFRACTIONf_chiral_restr0.065476
X-RAY DIFFRACTIONf_plane_restr0.003600
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1813-2.23580.34271010.2215939X-RAY DIFFRACTION66
2.2358-2.29630.26921340.20771262X-RAY DIFFRACTION90
2.2963-2.36380.26081360.20521364X-RAY DIFFRACTION95
2.3638-2.44010.30281340.19991361X-RAY DIFFRACTION96
2.4401-2.52730.28851320.20691389X-RAY DIFFRACTION97
2.5273-2.62850.28841420.20241397X-RAY DIFFRACTION98
2.6285-2.74810.27751370.18061395X-RAY DIFFRACTION98
2.7481-2.8930.25911420.17911395X-RAY DIFFRACTION98
2.893-3.07410.22331500.16921412X-RAY DIFFRACTION99
3.0741-3.31140.22751480.17111421X-RAY DIFFRACTION100
3.3114-3.64440.20821450.17151438X-RAY DIFFRACTION100
3.6444-4.17130.22341500.15131443X-RAY DIFFRACTION100
4.1713-5.25360.17491500.14461451X-RAY DIFFRACTION100
5.2536-40.23320.20011500.17621509X-RAY DIFFRACTION100
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)
1refined0.2322-1.0141-0.86482.2867-0.09781.1523-0.0122-0.2677-0.08770.1618-0.0108-0.06510.00940.23680.01160.2230.06750.01350.3845-0.00110.283125.67510.4970.9726
21.3320.5874-0.90352.63620.18242.55430.1116-0.26770.2686-0.0938-0.07120.0198-0.1792-0.00280.02090.21580.00920.00040.3183-0.01730.2836
30.8929-0.6855-0.47381.66160.92982.4912-0.00320.11450.010.0054-0.03560.13640.02660.03450.01170.1981-0.01260.02530.3501-0.03210.2427
41.8738-0.67350.69741.5435-0.58031.63350.15280.16080.00460.0426-0.0186-0.0257-0.0331-0.0698-0.10420.24210.01650.01650.4009-0.02910.344
53.4449-0.40431.51221.6454-1.07191.804-0.45550.00770.53520.07090.024-0.4063-0.1730.16520.27950.28040.0208-0.00760.3215-0.01670.3196
61.82070.1072-0.58942.20090.48970.43510.0699-0.1098-0.27020.1404-0.0683-0.13520.42840.05570.01290.26140.0080.01670.3636-0.00830.2798
71.65090.50260.11552.82310.35941.1324-0.1830.3074-0.1147-0.2390.1671-0.29770.07380.1554-0.04450.2654-0.02820.02350.3855-0.00750.2712
82.37950.2953-0.27250.3702-0.9820.6361-0.1255-0.52860.03620.14660.1090.0412-0.0776-0.1470.00870.25340.00610.05170.4335-0.04520.3281
Refinement TLS groupSelection details: chain D and (resseq 53:98))

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