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- PDB-3oaj: CRYSTAL STRUCTURE OF putative dioxygenase from Bacillus subtilis ... -

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Basic information

Entry
Database: PDB / ID: 3oaj
TitleCRYSTAL STRUCTURE OF putative dioxygenase from Bacillus subtilis subsp. subtilis str. 168
ComponentsPutative ring-cleaving dioxygenase mhqO
Keywordsstructural genomics / unknown function / PROTEIN STRUCTURE INITIATIVE / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen / : / dioxygenase activity / response to toxic substance / metal ion binding / cytoplasm
Similarity search - Function
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 ring-cleaving dioxygenase MhqO
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsMalashkevich, V.N. / Toro, R. / Seidel, R. / Garrett, S. / Foti, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF putative dioxygenase from Bacillus subtilis subsp. subtilis str. 168
Authors: Malashkevich, V.N. / Toro, R. / Seidel, R. / Garrett, S. / Foti, R. / Almo, S.C.
History
DepositionAug 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...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 / 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_asym_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_asym_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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative ring-cleaving dioxygenase mhqO
B: Putative ring-cleaving dioxygenase mhqO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3646
Polymers76,0412
Non-polymers3234
Water12,520695
1
A: Putative ring-cleaving dioxygenase mhqO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1823
Polymers38,0201
Non-polymers1612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative ring-cleaving dioxygenase mhqO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1823
Polymers38,0201
Non-polymers1612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.215, 86.181, 72.968
Angle α, β, γ (deg.)90.000, 91.650, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A-99999 - 99999
2111B-99999 - 99999

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Components

#1: Protein Putative ring-cleaving dioxygenase mhqO


Mass: 38020.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU05490, CAB12356.1, mhqO, ydfO / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL
References: UniProt: P96693, Oxidoreductases; Acting on single donors with incorporation of molecular oxygen (oxygenases); With incorporation of two atoms of oxygen
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 695 / 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: 2.08 Å3/Da / Density % sol: 40.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 30% PEG4000, 0.2 M ammonium sulfate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 112088 / % possible obs: 91.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.057 / Χ2: 1.142 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.4-1.424.30.69743010.70771
1.42-1.454.70.74853100.77787.8
1.45-1.4850.58256341.12392.3
1.48-1.515.20.58758630.75996.7
1.51-1.545.40.48860271.20599.5
1.54-1.585.50.40960930.7799.9
1.58-1.625.60.33560930.812100
1.62-1.665.50.28561090.841100
1.66-1.715.60.23460230.864100
1.71-1.765.60.19160870.879100
1.76-1.835.60.14761140.908100
1.83-1.95.40.12253410.99788.3
1.9-1.994.80.11847582.06377.8
1.99-2.095.60.07561441.199100
2.09-2.225.50.06155191.21191.1
2.22-2.395.10.06540841.9366.7
2.39-2.635.60.05361131.78199.9
2.63-3.025.50.04361161.704100
3.02-3.85.10.0347311.38177
3.8-505.60.02656281.23590.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 55.3 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å43.37 Å
Translation2.5 Å43.37 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZSW

1zsw


Resolution: 1.4→8 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.212 / WRfactor Rwork: 0.1716 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.843 / SU B: 2.829 / SU ML: 0.05 / SU R Cruickshank DPI: 0.0858 / SU Rfree: 0.0767 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2246 5602 5 %RANDOM
Rwork0.1797 ---
obs0.1819 111391 92.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 86.53 Å2 / Biso mean: 17.4305 Å2 / Biso min: 7.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4926 0 12 695 5633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225136
X-RAY DIFFRACTIONr_angle_refined_deg1.2631.9426982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4225638
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.2224.228272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05915823
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6661532
X-RAY DIFFRACTIONr_chiral_restr0.0860.2722
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214070
X-RAY DIFFRACTIONr_mcbond_it1.2533.53086
X-RAY DIFFRACTIONr_mcangle_it2.617504974
X-RAY DIFFRACTIONr_scbond_it3.817502050
X-RAY DIFFRACTIONr_scangle_it1.6344.51998
X-RAY DIFFRACTIONr_rigid_bond_restr0.81535136
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2443 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
TIGHT POSITIONAL0.335
TIGHT THERMAL1.2510
LS refinement shellResolution: 1.402→1.438 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 345 -
Rwork0.336 6758 -
all-7103 -
obs--81.82 %
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)
10.35590.1207-0.09810.6074-0.11540.18270.00460.010.00430.01240.0010.0383-0.0146-0.0062-0.00570.01750.0016-0.0090.02240.00040.008243.404510.526239.2518
20.39380.10470.10380.7010.13490.3046-0.00620.0371-0.0064-0.04060.0208-0.0469-0.00510.0139-0.01470.02940.00150.01010.03810.00180.005555.813716.38673.0479
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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