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- PDB-3ghj: Crystal structure from the mobile metagenome of Halifax Harbour S... -

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Basic information

Entry
Database: PDB / ID: 3ghj
TitleCrystal structure from the mobile metagenome of Halifax Harbour Sewage Outfall: Integron Cassette Protein HFX_CASS4
ComponentsPutative integron gene cassette protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Integron Cassette Protein / Mobile Metagenome / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Roll / Alpha Beta
Similarity search - Domain/homology
Putative integron gene cassette protein
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.471 Å
AuthorsSureshan, V. / Deshpande, C. / Harrop, S.J. / Kudritska, M. / Koenig, J.E. / Evdokimova, E. / Kim, Y. / Edwards, A.M. / Savchenko, A. / Joachimiak, A. ...Sureshan, V. / Deshpande, C. / Harrop, S.J. / Kudritska, M. / Koenig, J.E. / Evdokimova, E. / Kim, Y. / Edwards, A.M. / Savchenko, A. / Joachimiak, A. / Doolittle, W.F. / 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 Halifax Harbour Sewage Outfall: Integron Cassette Protein HFX_CASS4
Authors: Sureshan, V. / Deshpande, C. / Harrop, S.J. / Kudritska, M. / Koenig, J.E. / Evdokimova, E. / Kim, Y. / Edwards, A.M. / Savchenko, A. / Joachimiak, A. / Doolittle, W.F. / Stokes, H.W. / ...Authors: Sureshan, V. / Deshpande, C. / Harrop, S.J. / Kudritska, M. / Koenig, J.E. / Evdokimova, E. / Kim, Y. / Edwards, A.M. / Savchenko, A. / Joachimiak, A. / Doolittle, W.F. / Stokes, H.W. / Curmi, P.M.G. / Mabbutt, B.C.
History
DepositionMar 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative integron gene cassette protein


Theoretical massNumber of molelcules
Total (without water)16,3331
Polymers16,3331
Non-polymers00
Water1,22568
1
A: Putative integron gene cassette protein

A: Putative integron gene cassette protein


Theoretical massNumber of molelcules
Total (without water)32,6662
Polymers32,6662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area3550 Å2
ΔGint-22.5 kcal/mol
Surface area10990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.001, 66.391, 80.822
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-125-

HOH

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Components

#1: Protein Putative integron gene cassette protein


Mass: 16332.780 Da / Num. of mol.: 1 / Mutation: L97Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: ORF1 / Plasmid: p15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: B0BGV9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.094 Å3/Da / Density % sol: 41.27 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2 M Ammonium sulfate, 25% PEG 4000, 0.1 M Na acetate pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97921 Å
DetectorType: SBC-3 / Detector: CCD / Date: Oct 12, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.47→50 Å / Num. obs: 23542 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 13.12 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Χ2: 1.524 / Net I/σ(I): 37.28
Reflection shellResolution: 1.47→1.5 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 4.07 / Num. unique all: 1127 / Rsym value: 0.344 / Χ2: 0.605 / % possible all: 95.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
HKL-3000data collection
HKL-2000data reduction
PHENIXAUTOSOLphasing
RefinementMethod to determine structure: SAD / Resolution: 1.471→24.319 Å / Occupancy max: 1 / Occupancy min: 0.26 / FOM work R set: 0.919 / SU ML: 0.14 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.183 1969 8.48 %random
Rwork0.168 ---
all0.169 23217 --
obs0.169 23217 98.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.531 Å2 / ksol: 0.442 e/Å3
Displacement parametersBiso max: 66.91 Å2 / Biso mean: 17.906 Å2 / Biso min: 6.97 Å2
Baniso -1Baniso -2Baniso -3
1-0.377 Å2-0 Å20 Å2
2---1.749 Å2-0 Å2
3---1.372 Å2
Refinement stepCycle: LAST / Resolution: 1.471→24.319 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1054 0 0 68 1122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111096
X-RAY DIFFRACTIONf_angle_d1.0741502
X-RAY DIFFRACTIONf_chiral_restr0.078153
X-RAY DIFFRACTIONf_plane_restr0.006203
X-RAY DIFFRACTIONf_dihedral_angle_d16.148405
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.471-1.5080.1871340.1391447158195
1.508-1.5490.1611360.1151487162397
1.549-1.5940.1531350.1171469160497
1.594-1.6460.1641400.1191480162098
1.646-1.7050.1461380.1251494163297
1.705-1.7730.1911380.1321488162698
1.773-1.8540.1521390.1371507164698
1.854-1.9510.1691410.141524166599
1.951-2.0730.1671420.14115401682100
2.073-2.2330.1541430.14715381681100
2.233-2.4580.1811440.1681556170099
2.458-2.8130.211420.1781532167499
2.813-3.5430.1921460.191562170899
3.543-24.3220.1971510.1941624177598

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