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- PDB-4z2t: Crystal Structure of 2-hydroxybiphenyl 3-monooxygenase W225Y from... -

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Basic information

Entry
Database: PDB / ID: 4z2t
TitleCrystal Structure of 2-hydroxybiphenyl 3-monooxygenase W225Y from Pseudomonas azelaica
Components2-hydroxybiphenyl-3-monooxygenase
KeywordsOXIDOREDUCTASE / flavin dependent oxygenase
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / FAD binding
Similarity search - Function
Glutaredoxin - #120 / Aromatic-ring hydroxylase, C-terminal / : / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / Glutaredoxin / FAD/NAD(P)-binding domain superfamily ...Glutaredoxin - #120 / Aromatic-ring hydroxylase, C-terminal / : / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / Glutaredoxin / FAD/NAD(P)-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 2-hydroxybiphenyl-3-monooxygenase
Similarity search - Component
Biological speciesPseudomonas nitroreducens HBP1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsKanteev, M. / Bregman-Cohen, A. / Fishman, A.
CitationJournal: Biochim.Biophys.Acta / Year: 2015
Title: A crystal structure of 2-hydroxybiphenyl 3-monooxygenase with bound substrate provides insights into the enzymatic mechanism.
Authors: Kanteev, M. / Bregman-Cohen, A. / Deri, B. / Shahar, A. / Adir, N. / Fishman, A.
History
DepositionMar 30, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Oct 28, 2015Group: Database references
Revision 1.3May 8, 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

Downloads & links

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Assembly

Deposited unit
A: 2-hydroxybiphenyl-3-monooxygenase
B: 2-hydroxybiphenyl-3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,8554
Polymers129,2842
Non-polymers1,5712
Water8,197455
1
B: 2-hydroxybiphenyl-3-monooxygenase
hetero molecules

B: 2-hydroxybiphenyl-3-monooxygenase
hetero molecules

A: 2-hydroxybiphenyl-3-monooxygenase
hetero molecules

A: 2-hydroxybiphenyl-3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,7118
Polymers258,5694
Non-polymers3,1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
crystal symmetry operation3_545x+1/2,y-1/2,z1
crystal symmetry operation4_545-x+1/2,y-1/2,-z1
2
A: 2-hydroxybiphenyl-3-monooxygenase
hetero molecules

A: 2-hydroxybiphenyl-3-monooxygenase
hetero molecules

B: 2-hydroxybiphenyl-3-monooxygenase
hetero molecules

B: 2-hydroxybiphenyl-3-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,7118
Polymers258,5694
Non-polymers3,1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
Buried area16560 Å2
ΔGint-61 kcal/mol
Surface area81980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.380, 130.580, 78.750
Angle α, β, γ (deg.)90.00, 98.79, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-719-

HOH

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Components

#1: Protein 2-hydroxybiphenyl-3-monooxygenase


Mass: 64642.188 Da / Num. of mol.: 2 / Mutation: W225Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas nitroreducens HBP1 (bacteria)
Gene: hbpA / Plasmid: pET9a / Production host: Escherichia coli (E. coli) / References: UniProt: O06647, EC: 1.14.13.44
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M sodium citrate and 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.56 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.56 Å / Relative weight: 1
ReflectionResolution: 2.45→59.19 Å / Num. obs: 54998 / % possible obs: 97.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 11.8

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→43.85 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.236 2791 5.08 %
Rwork0.2178 --
obs0.2188 54971 97.05 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.228 Å2 / ksol: 0.362 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.5496 Å2-0 Å22.233 Å2
2---1.8949 Å2-0 Å2
3---8.4445 Å2
Refinement stepCycle: LAST / Resolution: 2.45→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8640 0 106 455 9201
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0238982
X-RAY DIFFRACTIONf_angle_d1.78412192
X-RAY DIFFRACTIONf_dihedral_angle_d15.8153264
X-RAY DIFFRACTIONf_chiral_restr0.3061340
X-RAY DIFFRACTIONf_plane_restr0.0091574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.49220.40841320.33922254X-RAY DIFFRACTION85
2.4922-2.53750.31611220.30522289X-RAY DIFFRACTION85
2.5375-2.58630.31121470.29542354X-RAY DIFFRACTION89
2.5863-2.63910.32131350.28342469X-RAY DIFFRACTION92
2.6391-2.69650.35471260.27752542X-RAY DIFFRACTION95
2.6965-2.75920.261360.25672623X-RAY DIFFRACTION97
2.7592-2.82820.26851180.24892662X-RAY DIFFRACTION99
2.8282-2.90470.27351380.24092694X-RAY DIFFRACTION100
2.9047-2.99010.26941430.22322649X-RAY DIFFRACTION100
2.9901-3.08660.28011440.2222685X-RAY DIFFRACTION100
3.0866-3.19690.27891460.23162675X-RAY DIFFRACTION100
3.1969-3.32490.25021540.21672671X-RAY DIFFRACTION100
3.3249-3.47610.22621320.21212701X-RAY DIFFRACTION100
3.4761-3.65930.21741320.21022718X-RAY DIFFRACTION100
3.6593-3.88840.20281380.20152692X-RAY DIFFRACTION100
3.8884-4.18850.19761620.18472667X-RAY DIFFRACTION100
4.1885-4.60950.19221380.16352708X-RAY DIFFRACTION100
4.6095-5.27560.16211310.16862707X-RAY DIFFRACTION100
5.2756-6.6430.21561440.21582712X-RAY DIFFRACTION100
6.643-43.85740.19431730.2152708X-RAY DIFFRACTION99

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