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- PDB-4z2r: Crystal structure of 2-hydroxybiphenyl 3-monooxygenase from Pseud... -

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Basic information

Entry
Database: PDB / ID: 4z2r
TitleCrystal structure of 2-hydroxybiphenyl 3-monooxygenase 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: 2.3 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 2.0Nov 18, 2020Group: Atomic model / Structure summary / Category: atom_site / struct / Item: _atom_site.occupancy / _struct.title
Revision 2.1May 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)130,9024
Polymers129,3302
Non-polymers1,5712
Water11,458636
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)261,8038
Polymers258,6614
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)261,8038
Polymers258,6614
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 area16270 Å2
ΔGint-62 kcal/mol
Surface area82540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.350, 131.490, 79.160
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
11B-969-

HOH

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Components

#1: Protein 2-hydroxybiphenyl-3-monooxygenase


Mass: 64665.219 Da / Num. of mol.: 2
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
#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.: 636 / 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: 59.98 %
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: May 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.56 Å / Relative weight: 1
ReflectionResolution: 2.3→43.95 Å / Num. obs: 67249 / % possible obs: 97.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 9.7
Reflection shellRmerge(I) obs: 0.081

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.3→29.271 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2584 3408 5.07 %
Rwork0.2336 --
obs0.2348 67211 97.02 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.826 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.4971 Å2-0 Å21.1516 Å2
2---2.5647 Å2-0 Å2
3---6.0618 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.271 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8680 0 106 636 9422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.028985
X-RAY DIFFRACTIONf_angle_d1.9712198
X-RAY DIFFRACTIONf_dihedral_angle_d15.8813260
X-RAY DIFFRACTIONf_chiral_restr0.1671341
X-RAY DIFFRACTIONf_plane_restr0.0121574
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33280.35251290.2972569X-RAY DIFFRACTION94
2.3328-2.36770.35371220.27632570X-RAY DIFFRACTION95
2.3677-2.40460.371500.28212604X-RAY DIFFRACTION94
2.4046-2.4440.30971450.27972550X-RAY DIFFRACTION95
2.444-2.48620.29791350.25752607X-RAY DIFFRACTION95
2.4862-2.53130.31091350.28122621X-RAY DIFFRACTION95
2.5313-2.580.29611430.27732587X-RAY DIFFRACTION95
2.58-2.63260.31281160.26822622X-RAY DIFFRACTION96
2.6326-2.68980.29361280.26312634X-RAY DIFFRACTION96
2.6898-2.75240.30311340.25612682X-RAY DIFFRACTION97
2.7524-2.82110.26741470.24192664X-RAY DIFFRACTION97
2.8211-2.89740.261490.24742659X-RAY DIFFRACTION98
2.8974-2.98250.25521490.24642647X-RAY DIFFRACTION98
2.9825-3.07870.26361520.23552680X-RAY DIFFRACTION98
3.0787-3.18860.26571430.23722681X-RAY DIFFRACTION98
3.1886-3.31610.23971500.22712673X-RAY DIFFRACTION98
3.3161-3.46680.25841540.2322701X-RAY DIFFRACTION98
3.4668-3.64930.25271310.22232725X-RAY DIFFRACTION99
3.6493-3.87740.22511450.21312701X-RAY DIFFRACTION99
3.8774-4.1760.23181510.19872696X-RAY DIFFRACTION99
4.176-4.59480.18451530.17142698X-RAY DIFFRACTION99
4.5948-5.25640.20311580.18212731X-RAY DIFFRACTION99
5.2564-6.60990.25931570.24372725X-RAY DIFFRACTION99
6.6099-29.27370.28571320.26512776X-RAY DIFFRACTION99

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