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- PDB-4cy6: apo structure of 2-hydroxybiphenyl 3-monooxygenase HbpA -

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Basic information

Entry
Database: PDB / ID: 4cy6
Titleapo structure of 2-hydroxybiphenyl 3-monooxygenase HbpA
Components2-HYDROXYBIPHENYL-3-MONOOXYGENASE
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / FAD / HYDROXYLATION / FLAVIN / NADH
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
2-hydroxybiphenyl-3-monooxygenase
Similarity search - Component
Biological speciesPSEUDOMONAS NITROREDUCENS HBP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsJensen, C.N. / Farrugia, J.E. / Frank, A. / Man, H. / Hart, S. / Turkenburg, J.P. / Grogan, G.
CitationJournal: Chembiochem / Year: 2015
Title: Structures of the Apo and Fad-Bound Forms of 2-Hydroxybiphenyl 3-Monooxygenase (Hbpa) Locate Activity Hotspots Identified by Using Directed Evolution.
Authors: Jensen, C.N. / Mielke, T. / Farrugia, J.E. / Frank, A. / Man, H. / Hart, S. / Turkenburg, J.P. / Grogan, G.
History
DepositionApr 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-HYDROXYBIPHENYL-3-MONOOXYGENASE
B: 2-HYDROXYBIPHENYL-3-MONOOXYGENASE
C: 2-HYDROXYBIPHENYL-3-MONOOXYGENASE
D: 2-HYDROXYBIPHENYL-3-MONOOXYGENASE


Theoretical massNumber of molelcules
Total (without water)255,4534
Polymers255,4534
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10240 Å2
ΔGint-34.2 kcal/mol
Surface area78960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.350, 94.670, 99.160
Angle α, β, γ (deg.)115.03, 96.09, 109.59
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9998, -0.01895, 0.007675), (0.01878, -0.703, 0.7109), (-0.008078, 0.7109, 0.7032)76.54, 58.82, -24.52
2given(-0.9639, 0.2455, -0.1029), (0.246, 0.6743, -0.6963), (-0.1016, -0.6965, -0.7103)65.8, 38.86, 116.9
3given(0.9655, -0.2394, 0.1022), (-0.2393, -0.9709, -0.01362), (0.1025, -0.0113, -0.9947)9.816, 115, 85.03

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Components

#1: Protein
2-HYDROXYBIPHENYL-3-MONOOXYGENASE


Mass: 63863.367 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS NITROREDUCENS HBP1 (bacteria)
Plasmid: PETYSBLIC-3C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O06647, EC: 1.14.13.44
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.54 Å3/Da / Density % sol: 51.5 % / Description: NONE
Crystal growpH: 5.5
Details: 18% (W/V) PEG 3350, 0.15 M KSCN IN BIS-TRIS PROPANE BUFFER AT PH 5.5, WITH A PROTEIN CONCENTRATION OF 10 MG ML-1.

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.76→85.97 Å / Num. obs: 59321 / % possible obs: 97.9 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.4
Reflection shellResolution: 2.76→2.83 Å / Redundancy: 2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.6 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
xia2data reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3IHG

3ihg


Resolution: 2.76→85.97 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.909 / SU B: 15.938 / SU ML: 0.309 / Cross valid method: THROUGHOUT / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24114 2967 5.1 %RANDOM
Rwork0.19 ---
obs0.19262 55716 96.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.665 Å2
Baniso -1Baniso -2Baniso -3
1--4.73 Å21.03 Å20.24 Å2
2--2.57 Å22.13 Å2
3----1.44 Å2
Refinement stepCycle: LAST / Resolution: 2.76→85.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16126 0 0 139 16265
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01916606
X-RAY DIFFRACTIONr_bond_other_d0.0060.0215467
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.95322624
X-RAY DIFFRACTIONr_angle_other_deg1.061335244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.46652210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28122.556622
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.59152379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.78715117
X-RAY DIFFRACTIONr_chiral_restr0.0910.22593
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02119185
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023838
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.1366.0268894
X-RAY DIFFRACTIONr_mcbond_other5.1366.0268893
X-RAY DIFFRACTIONr_mcangle_it7.3969.04611086
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.6216.3987712
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.76→2.832 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 217 -
Rwork0.323 4031 -
obs--94.42 %

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