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- PDB-4z2u: Crystal Structure of 2-hydroxybiphenyl 3-monooxygenase R242Q from... -

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Basic information

Entry
Database: PDB / ID: 4z2u
TitleCrystal Structure of 2-hydroxybiphenyl 3-monooxygenase R242Q 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 / Resolution: 2.5 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 2.0May 8, 2024Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.occupancy / _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)130,8434
Polymers129,2722
Non-polymers1,5712
Water11,656647
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)261,6878
Polymers258,5454
Non-polymers3,1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
crystal symmetry operation4_455-x-1/2,y+1/2,-z1
MethodPISA
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)261,6878
Polymers258,5454
Non-polymers3,1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation3_545x+1/2,y-1/2,z1
crystal symmetry operation4_445-x-1/2,y-1/2,-z1
Buried area16480 Å2
ΔGint-62 kcal/mol
Surface area83010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.140, 131.540, 79.000
Angle α, β, γ (deg.)90.00, 98.28, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-951-

HOH

21A-987-

HOH

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Components

#1: Protein 2-hydroxybiphenyl-3-monooxygenase


Mass: 64636.156 Da / Num. of mol.: 2 / Mutation: R242Q
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.: 647 / 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: 3.07 Å3/Da / Density % sol: 59.87 %
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: Dec 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.56 Å / Relative weight: 1
ReflectionResolution: 2.5→42.14 Å / Num. obs: 49676 / % possible obs: 92.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 20.7
Reflection shellRmerge(I) obs: 0.191

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.5→32.373 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2373 2527 5.09 %
Rwork0.2037 --
obs0.2054 49652 92.18 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.404 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.5181 Å20 Å21.6223 Å2
2---2.0587 Å2-0 Å2
3---11.5699 Å2
Refinement stepCycle: LAST / Resolution: 2.5→32.373 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8660 0 106 647 9413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088984
X-RAY DIFFRACTIONf_angle_d1.30412198
X-RAY DIFFRACTIONf_dihedral_angle_d14.4573258
X-RAY DIFFRACTIONf_chiral_restr0.131340
X-RAY DIFFRACTIONf_plane_restr0.0051574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.54810.32341100.30032169X-RAY DIFFRACTION76
2.5481-2.60010.33181210.29522230X-RAY DIFFRACTION79
2.6001-2.65660.32321230.27612327X-RAY DIFFRACTION82
2.6566-2.71840.28031260.25732381X-RAY DIFFRACTION84
2.7184-2.78630.26521320.2552427X-RAY DIFFRACTION87
2.7863-2.86160.32251210.25062543X-RAY DIFFRACTION89
2.8616-2.94570.2891590.23992550X-RAY DIFFRACTION91
2.9457-3.04080.2591340.22192652X-RAY DIFFRACTION94
3.0408-3.14930.26621430.21732719X-RAY DIFFRACTION96
3.1493-3.27530.26461620.2122755X-RAY DIFFRACTION97
3.2753-3.42420.23611550.20052730X-RAY DIFFRACTION98
3.4242-3.60460.23061250.192816X-RAY DIFFRACTION98
3.6046-3.83010.22171630.18712752X-RAY DIFFRACTION98
3.8301-4.12520.21091380.17532826X-RAY DIFFRACTION99
4.1252-4.53940.17191570.15372780X-RAY DIFFRACTION98
4.5394-5.19390.20841690.15632780X-RAY DIFFRACTION99
5.1939-6.53490.22351470.2092837X-RAY DIFFRACTION98
6.5349-32.37570.20371420.19562851X-RAY DIFFRACTION98

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