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- PDB-3qvm: The structure of olei00960, a hydrolase from Oleispira antarctica -

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Basic information

Entry
Database: PDB / ID: 3qvm
TitleThe structure of olei00960, a hydrolase from Oleispira antarctica
ComponentsOlei00960
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / alpha-beta hydrolase fold
Function / homologyalpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Olei00960
Function and homology information
Biological speciesOleispira antarctica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / PHASER / Resolution: 1.998 Å
AuthorsSinger, A.U. / Kagan, O. / Kim, Y. / Edwards, A.M. / Joachimiak, A. / Savchenko, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Nat Commun / Year: 2013
Title: Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica.
Authors: Kube, M. / Chernikova, T.N. / Al-Ramahi, Y. / Beloqui, A. / Lopez-Cortez, N. / Guazzaroni, M.E. / Heipieper, H.J. / Klages, S. / Kotsyurbenko, O.R. / Langer, I. / Nechitaylo, T.Y. / ...Authors: Kube, M. / Chernikova, T.N. / Al-Ramahi, Y. / Beloqui, A. / Lopez-Cortez, N. / Guazzaroni, M.E. / Heipieper, H.J. / Klages, S. / Kotsyurbenko, O.R. / Langer, I. / Nechitaylo, T.Y. / Lunsdorf, H. / Fernandez, M. / Juarez, S. / Ciordia, S. / Singer, A. / Kagan, O. / Egorova, O. / Alain Petit, P. / Stogios, P. / Kim, Y. / Tchigvintsev, A. / Flick, R. / Denaro, R. / Genovese, M. / Albar, J.P. / Reva, O.N. / Martinez-Gomariz, M. / Tran, H. / Ferrer, M. / Savchenko, A. / Yakunin, A.F. / Yakimov, M.M. / Golyshina, O.V. / Reinhardt, R. / Golyshin, P.N.
History
DepositionFeb 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Aug 7, 2013Group: Database references
Revision 1.4Jul 17, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.7Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Olei00960
B: Olei00960
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,62811
Polymers63,0272
Non-polymers6029
Water4,324240
1
A: Olei00960
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8245
Polymers31,5131
Non-polymers3114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Olei00960
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8046
Polymers31,5131
Non-polymers2915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.067, 123.067, 49.218
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Olei00960


Mass: 31513.275 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: TEV cleavage after purification / Source: (gene. exp.) Oleispira antarctica (bacteria) / Gene: Olei00960 / Plasmid: p15Tvlic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: U3KRE9*PLUS

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Non-polymers , 5 types, 249 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.96 Å3/Da / Density % sol: 58.4 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05M Calcium Chloride, 0.1M Bis-Tris pH6.5, 1.6M Ammonium Sulfate. Cryoprotected with Paratone-N oil, 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: 0.97918 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 10, 2009 / Details: mirrors
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 50364 / Num. obs: 50298 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 24.75
Reflection shellResolution: 2→2.03 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 4.13 / Num. unique all: 2463 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX1.6_289refinement
PHASERphasing
REFMAC5.2.0019 plus PHENIX (phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-3000data collection
RefinementMethod to determine structure: PHASER
Starting model: Model based on 1wom

1wom


Resolution: 1.998→30.767 Å / σ(F): 0.91 / Phase error: 27.56 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1847 3906 4.03 %RANDOM
Rwork0.1558 ---
obs0.1571 96971 99.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.924 Å2 / ksol: 0.368 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.3106 Å2-0 Å20 Å2
2---3.3106 Å2-0 Å2
3---6.6212 Å2
Refinement stepCycle: LAST / Resolution: 1.998→30.767 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4265 0 29 240 4534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074427
X-RAY DIFFRACTIONf_angle_d0.9646019
X-RAY DIFFRACTIONf_dihedral_angle_d17.3421578
X-RAY DIFFRACTIONf_chiral_restr0.069683
X-RAY DIFFRACTIONf_plane_restr0.004779
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.9982-2.03260.27581890.2214355454490
2.0326-2.06950.28871930.21394620481393
2.0695-2.10930.24351910.20854550474194
2.1093-2.15230.25141860.20114674486095
2.1523-2.1990.17861960.19354570476695
2.199-2.25010.22581890.18984679486895
2.2501-2.30620.23541920.18244608480095
2.3062-2.36850.19372060.17524733493995
2.3685-2.4380.24611960.17354638483496
2.438-2.51650.2311960.16914642483896
2.5165-2.60620.19741870.16844709489696
2.6062-2.71030.19681910.16914701489296
2.7103-2.83330.22692000.1524644484496
2.8333-2.98210.17782020.16154689489196
2.9821-3.16810.20012020.15984708491096
3.1681-3.41130.17021910.14954698488996
3.4113-3.75210.1581940.13184695488996
3.7521-4.28930.12631900.11654701489196
4.2893-5.38270.14062000.10984686488696
5.3827-18.71350.14141930.14474692488596

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