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- PDB-5brt: Crystal Structure of 2-hydroxybiphenyl 3-monooxygenase from Pseud... -

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Basic information

Entry
Database: PDB / ID: 5brt
TitleCrystal Structure of 2-hydroxybiphenyl 3-monooxygenase from Pseudomonas azelaica with 2-hydroxybiphenyl in the active site
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
Aromatic-ring hydroxylase, C-terminal / Glutaredoxin - #120 / 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
2-HYDROXYBIPHENYL / FLAVIN-ADENINE DINUCLEOTIDE / 2-hydroxybiphenyl-3-monooxygenase
Similarity search - Component
Biological speciesPseudomonas nitroreducens HBP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKanteev, M. / Bregman-Cohen, A. / Deri, B. / Adir, N. / 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
DepositionJun 1, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Structure summary
Revision 1.2Oct 28, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)129,5846
Polymers127,6732
Non-polymers1,9124
Water15,133840
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)259,16812
Polymers255,3454
Non-polymers3,8238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
crystal symmetry operation3_555x+1/2,y+1/2,z1
crystal symmetry operation4_555-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)259,16812
Polymers255,3454
Non-polymers3,8238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation3_445x-1/2,y-1/2,z1
crystal symmetry operation4_545-x+1/2,y-1/2,-z1
Buried area18690 Å2
ΔGint-77 kcal/mol
Surface area80540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.470, 130.680, 78.660
Angle α, β, γ (deg.)90.000, 98.610, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-869-

HOH

21A-1100-

HOH

31B-791-

HOH

41B-1020-

HOH

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Components

#1: Protein 2-hydroxybiphenyl-3-monooxygenase


Mass: 63836.336 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: isolated from a genetically manipulated source
Formula: C27H33N9O15P2
Source: (gene. exp.) Pseudomonas nitroreducens HBP1 (bacteria)
Gene: hbpA / Plasmid: pET9a / Production host: Escherichia coli (E. coli) / References: EC: 1.14.13.44 / Comment: FAD*YM
#3: Chemical ChemComp-CH9 / 2-HYDROXYBIPHENYL / 1,1'-BIPHENYL-2-OL / 2-PHENYLPHENOL


Mass: 170.207 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H10O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 840 / 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: 3.05 Å3/Da / Density % sol: 59.73 %
Crystal growTemperature: 298 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: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→99.021 Å / Num. all: 102878 / Num. obs: 102878 / % possible obs: 99.6 % / Redundancy: 4.9 % / Biso Wilson estimate: 23.48 Å2 / Rpim(I) all: 0.02 / Rrim(I) all: 0.044 / Rsym value: 0.039 / Net I/av σ(I): 12.687 / Net I/σ(I): 26.5 / Num. measured all: 501762
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2-2.115.30.1674.878901149630.0790.16710.199.2
2.11-2.245.20.1117.273197141630.0530.11113.899.5
2.24-2.395.10.0799.867449132810.0380.07917.999.4
2.39-2.5850.0612.462130124090.0290.0622.599.7
2.58-2.834.90.04515.355608114340.0230.04528.299.8
2.83-3.164.70.03617.949429104130.0180.03635.199.9
3.16-3.654.60.0319.24191891580.0150.0342.299.9
3.65-4.474.50.02820.83451177550.0140.02847100
4.47-6.324.20.02720.22519960180.0140.02745.999.9
6.32-36.3044.10.02520.51342032840.0140.02545.498.3

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4z2r

4z2r


Resolution: 2.3→36.304 Å / FOM work R set: 0.8132 / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2546 3348 4.96 %
Rwork0.2291 64215 -
obs0.2304 67563 99.36 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.053 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 276.96 Å2 / Biso mean: 33.21 Å2 / Biso min: 5.57 Å2
Baniso -1Baniso -2Baniso -3
1--6.7471 Å2-0 Å23.1243 Å2
2---1.0802 Å2-0 Å2
3---7.8273 Å2
Refinement stepCycle: final / Resolution: 2.3→36.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8563 0 132 840 9535
Biso mean--37.09 33.46 -
Num. residues----1113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098903
X-RAY DIFFRACTIONf_angle_d1.35212083
X-RAY DIFFRACTIONf_chiral_restr0.1191328
X-RAY DIFFRACTIONf_plane_restr0.0061555
X-RAY DIFFRACTIONf_dihedral_angle_d13.8573215
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.33290.31611450.24882637278299
2.3329-2.36770.30131270.23862659278699
2.3677-2.40470.24381390.2382652279199
2.4047-2.44410.25311480.22692630277899
2.4441-2.48620.2741290.22872641277099
2.4862-2.53140.29021420.23392676281899
2.5314-2.58010.30811300.23712657278799
2.5801-2.63270.3091490.22912683283299
2.6327-2.690.2771310.23362678280999
2.69-2.75250.27361260.23472667279399
2.7525-2.82130.28541400.22832655279599
2.8213-2.89760.26621480.23192677282599
2.8976-2.98280.2581370.21562661279899
2.9828-3.0790.23281430.21226672810100
3.079-3.1890.2671370.219526892826100
3.189-3.31660.21671520.21426762828100
3.3166-3.46750.24321280.213127132841100
3.4675-3.65010.20961430.214226932836100
3.6501-3.87860.23361440.209426782822100
3.8786-4.17760.22231540.207826772831100
4.1776-4.59730.20781580.200326872845100
4.5973-5.26080.23181430.215927132856100
5.2608-6.62150.31051270.279127182845100
6.6215-36.30860.34641280.32252731285998
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)
11.1261-0.3192-0.0020.7697-0.19970.39240.09290.0630.1809-0.1081-0.1140.14-0.0002-0.02470.05190.088-0.0132-0.00040.0908-0.00680.128212.1326-42.6553-2.1722
21.083-0.7673-0.37931.2411-0.31270.81030.09130.25390.0546-0.3413-0.1990.25340.0770.01350.11310.15570.0086-0.03230.12440.01570.209216.6568-37.3224-9.038
30.8090.1050.14361.32020.32430.50850.0764-0.10860.15380.045-0.17870.01140.06260.010.00410.0622-0.02960.02710.0772-0.0246-0.162427.3676-51.54246.592
41.1231-0.39560.05240.84440.09050.43450.08220.0762-0.1193-0.1145-0.1204-0.1576-0.02760.0190.05140.0869-0.00240.01220.09220.01220.11264.7174-24.9572-2.2813
51.1089-0.80610.12971.7605-0.27391.07170.1460.30420.047-0.3651-0.2666-0.4796-0.10890.00250.04630.21810.04260.04540.1761-0.04670.291363.8937-30.0607-14.3295
60.79080.0072-0.09051.3286-0.21380.47940.088-0.062-0.2997-0.0047-0.1316-0.0222-0.0639-0.0177-0.01140.0569-0.0354-0.00740.08130.0067-0.096550.009-20.11835.0232
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:150)A5 - 150
2X-RAY DIFFRACTION2chain 'A' and (resseq 151:377)A151 - 377
3X-RAY DIFFRACTION3chain 'A' and (resseq 378:585)A378 - 585
4X-RAY DIFFRACTION4chain 'B' and (resseq 5:149)B5 - 149
5X-RAY DIFFRACTION5chain 'B' and (resseq 150:307)B150 - 307
6X-RAY DIFFRACTION6chain 'B' and (resseq 308:585)B308 - 585

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