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- PDB-3ihm: Structure of the oxygenase component of a Pseudomonas styrene mon... -

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Basic information

Entry
Database: PDB / ID: 3ihm
TitleStructure of the oxygenase component of a Pseudomonas styrene monooxygenase
ComponentsStyrene monooxygenase A
KeywordsOXIDOREDUCTASE / Rossmann fold / anti-parallel beta strands / dimer / cavity
Function / homology
Function and homology information


monooxygenase activity
Similarity search - Function
D-Amino Acid Oxidase; Chain A, domain 2 - #40 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #650 / Styrene monooxygenase StyA, putative substrate binding domain / Styrene monooxygenase A putative substrate binding domain / D-Amino Acid Oxidase; Chain A, domain 2 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / Helix non-globular / 3-Layer(bba) Sandwich ...D-Amino Acid Oxidase; Chain A, domain 2 - #40 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #650 / Styrene monooxygenase StyA, putative substrate binding domain / Styrene monooxygenase A putative substrate binding domain / D-Amino Acid Oxidase; Chain A, domain 2 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / Helix non-globular / 3-Layer(bba) Sandwich / Special / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Styrene monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS, molecular replacement / MIRAS / molecular replacement / Resolution: 2.3 Å
AuthorsRosenzweig, A.C. / Ukaegbu, U.E. / Gassner, G.
CitationJournal: Biochemistry / Year: 2010
Title: Structure and ligand binding properties of the epoxidase component of styrene monooxygenase
Authors: Ukaegbu, U.E. / Kantz, A. / Beaton, M. / Gassner, G.T. / Rosenzweig, A.C.
History
DepositionJul 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Styrene monooxygenase A
B: Styrene monooxygenase A


Theoretical massNumber of molelcules
Total (without water)96,2302
Polymers96,2302
Non-polymers00
Water10,413578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Styrene monooxygenase A


Theoretical massNumber of molelcules
Total (without water)48,1151
Polymers48,1151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Styrene monooxygenase A


Theoretical massNumber of molelcules
Total (without water)48,1151
Polymers48,1151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)114.302, 114.302, 140.803
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Styrene monooxygenase A


Mass: 48115.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: S12 / Production host: Escherichia coli (E. coli) / References: UniProt: O33471*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 578 / 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: 2.91 Å3/Da / Density % sol: 57.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M MgCl2, 0.1 M Tris-HCl, pH 8.5, 30% (w/v) PEG-4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-D11.03
SYNCHROTRONAPS 21-ID-F20.98
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDDec 1, 2008
MAR CCD 130 mm2CCDJun 4, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1graphiteSINGLE WAVELENGTHMx-ray1
2graphiteSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.031
20.981
ReflectionRedundancy: 8 % / Av σ(I) over netI: 30.88 / Number: 168337 / Rmerge(I) obs: 0.126 / Χ2: 1.94 / D res high: 3 Å / D res low: 50 Å / Num. obs: 21093 / % possible obs: 98.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.465096.710.0544.2018
5.136.4699.210.0782.4668.2
4.485.1399.710.0782.68.1
4.074.4899.610.0942.1568.1
3.784.0799.710.1321.8418.1
3.563.7899.410.1821.5778.1
3.383.5699.510.2691.288.1
3.233.3899.210.3921.1058
3.113.2398.710.5251.027.9
33.1196.910.6940.9567.1
ReflectionResolution: 2.27→50 Å / Num. obs: 48378 / % possible obs: 100 % / Redundancy: 11.6 % / Rmerge(I) obs: 0.093 / Χ2: 1.204 / Net I/σ(I): 8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.27-2.3111.60.37823980.7281,2100
2.31-2.3511.60.35124020.7321,2100
2.35-2.411.60.31224120.7481,2100
2.4-2.4511.60.27724210.7341,2100
2.45-2.511.60.25123940.7511,2100
2.5-2.5611.60.21424190.7211,2100
2.56-2.6211.60.19623990.7391,2100
2.62-2.6911.60.17924100.7331,2100
2.69-2.7711.60.15924170.751,2100
2.77-2.8611.60.13724370.7841,2100
2.86-2.9611.60.12223980.7881,2100
2.96-3.0811.60.10224240.8271,2100
3.08-3.2211.60.08624120.9431,2100
3.22-3.3911.60.08524011.2941,2100
3.39-3.611.60.08424371.8881,2100
3.6-3.8811.50.07924172.261,2100
3.88-4.2711.40.07624372.6361,2100
4.27-4.8911.40.05524172.2031,2100
4.89-6.1611.60.04224471.2771,2100
6.16-5011.20.03624792.5911,299.9

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Phasing

Phasing
Method
MIRAS
molecular replacement
Phasing MRRfactor: 34.2 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.27 Å42.41 Å
Translation2.27 Å42.41 Å
Phasing MIR derResolution: 0→0.24 Å / Power acentric: 0.11 / Power centric: 3.02 / Reflection acentric: 18 / Reflection centric: 3
Phasing MIR der shellHighest resolution: 0 Å / Lowest resolution: 0.24 Å / Power acentric: 0.42 / Power centric: 8.92 / Reflection acentric: 2 / Reflection centric: 12

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.2phasing
SHARPphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
RefinementMethod to determine structure: MIRAS, molecular replacement / Resolution: 2.3→42.41 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.909 / WRfactor Rfree: 0.233 / WRfactor Rwork: 0.196 / Occupancy max: 1 / Occupancy min: 1 / SU B: 14.625 / SU ML: 0.161 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.32 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.244 2340 5.1 %RANDOM
Rwork0.206 ---
obs0.207 46247 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 76.37 Å2 / Biso mean: 18.854 Å2 / Biso min: 2.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å20 Å2
2--0.06 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.3→42.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6429 0 0 578 7007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226585
X-RAY DIFFRACTIONr_angle_refined_deg0.8911.9588931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8475813
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.53523.62326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.283151066
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5431550
X-RAY DIFFRACTIONr_chiral_restr0.0610.2959
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215128
X-RAY DIFFRACTIONr_mcbond_it0.1791.54047
X-RAY DIFFRACTIONr_mcangle_it0.34626484
X-RAY DIFFRACTIONr_scbond_it0.44332538
X-RAY DIFFRACTIONr_scangle_it0.7864.52447
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.266-2.3250.2871600.2463372357298.88
2.325-2.3880.31910.2483291348599.914
2.388-2.4580.2941730.2493193336899.941
2.458-2.5330.2841510.2453128328099.97
2.533-2.6160.3151700.2442995316899.905
2.616-2.7080.2961580.2532947310699.968
2.708-2.810.2831500.2522792294699.864
2.81-2.9250.2871620.2412732289799.896
2.925-3.0550.3151200.22825872707100
3.055-3.2040.2441350.21825132648100
3.204-3.3770.2721070.2062393250199.96
3.377-3.5810.2351200.18722452365100
3.581-3.8280.2131180.18221042222100
3.828-4.1340.2151220.18119482070100
4.134-4.5280.241900.17118291919100
4.528-5.0610.191880.17816431731100
5.061-5.8420.255780.20814521530100
5.842-7.1480.22710.2191225129799.923
7.148-10.0830.178510.1729591010100
10.083-99.0150.213270.19553257297.727
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)
10.35060.2239-0.09370.6011-0.11830.63640.0164-0.02660.0041-0.0225-0.0232-0.0459-0.0108-0.08680.00680.01080.0019-0.01240.026-0.00640.041531.8318-25.6625-20.6204
20.3617-0.06090.06430.5415-0.00080.78690.05840.0270.03770.0254-0.0039-0.00980.0565-0.0454-0.05450.0350.0141-0.01350.0144-0.00540.02541.31095.95153.958
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 410
2X-RAY DIFFRACTION1A411 - 697
3X-RAY DIFFRACTION2B4 - 410
4X-RAY DIFFRACTION2B411 - 701

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