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- PDB-1ykj: A45G p-hydroxybenzoate hydroxylase with p-hydroxybenzoate bound -

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Basic information

Entry
Database: PDB / ID: 1ykj
TitleA45G p-hydroxybenzoate hydroxylase with p-hydroxybenzoate bound
ComponentsP-hydroxybenzoate hydroxylase
KeywordsOXIDOREDUCTASE / phbh / catalysis / conformations
Function / homology
Function and homology information


4-hydroxybenzoate 3-monooxygenase (NADPH) activity / 4-hydroxybenzoate 3-monooxygenase / 4-hydroxybenzoate 3-monooxygenase activity / benzoate catabolic process via hydroxylation / FAD binding / flavin adenine dinucleotide binding / oxidoreductase activity
Similarity search - Function
4-hydroxybenzoate 3-monooxygenase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / P-HYDROXYBENZOIC ACID / PYROSULFATE / p-hydroxybenzoate hydroxylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCole, L.J. / Gatti, D.L. / Entsch, B. / Ballou, D.P.
CitationJournal: Biochemistry / Year: 2005
Title: Removal of a methyl group causes global changes in p-hydroxybenzoate hydroxylase.
Authors: Cole, L.J. / Gatti, D.L. / Entsch, B. / Ballou, D.P.
History
DepositionJan 18, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 600HETEROGEN PSL is pyrosulfate (S2O7(2-)). The map is clear, however pyrosulfate was not added to the ...HETEROGEN PSL is pyrosulfate (S2O7(2-)). The map is clear, however pyrosulfate was not added to the holding solution. It could have been a contamination from ammonium sulfate. It could also be pyrophosphate, possibly originating from a degradation of FAD. However, it is impossible to discriminate between pyrosulfate or pyrophosphate based on the map or the refinement).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P-hydroxybenzoate hydroxylase
B: P-hydroxybenzoate hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,08920
Polymers88,7372
Non-polymers3,35218
Water9,764542
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8900 Å2
ΔGint-180 kcal/mol
Surface area30060 Å2
MethodPISA
2
A: P-hydroxybenzoate hydroxylase
B: P-hydroxybenzoate hydroxylase
hetero molecules

A: P-hydroxybenzoate hydroxylase
B: P-hydroxybenzoate hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,17940
Polymers177,4744
Non-polymers6,70536
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area21340 Å2
ΔGint-369 kcal/mol
Surface area56560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.860, 85.897, 146.074
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-3447-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein P-hydroxybenzoate hydroxylase / 4-hydroxybenzoate 3-monooxygenase / PHBH


Mass: 44368.523 Da / Num. of mol.: 2 / Mutation: A45G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pobA / Plasmid: pIE130 (a derivative of pUC18) / Production host: Escherichia coli (E. coli) / Strain (production host): JM105
References: UniProt: P20586, 4-hydroxybenzoate 3-monooxygenase

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Non-polymers , 5 types, 560 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-PHB / P-HYDROXYBENZOIC ACID


Mass: 138.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O3
#5: Chemical ChemComp-PSL / PYROSULFATE


Mass: 176.126 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O7S2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 542 / 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: 2.47 Å3/Da / Density % sol: 45.14 %
Crystal growTemperature: 310 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: ammonium sulfate, tris-sulfate, fad, edta, glutathion, sodium sulfite, p-hydroxybenzoate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: Osmic confocal
RadiationMonochromator: Osmic confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.74→31.6 Å / Num. all: 76039 / Num. obs: 76039 / % possible obs: 84 % / Observed criterion σ(I): 1 / Redundancy: 11.89 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 4.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1IUW

1iuw


Resolution: 2→31.51 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 446344.11 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.265 6131 10.2 %RANDOM
Rwork0.201 ---
obs0.201 59975 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 83.6505 Å2 / ksol: 0.402482 e/Å3
Displacement parametersBiso mean: 38.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.32 Å20 Å20 Å2
2--1.77 Å20 Å2
3----3.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2→31.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6212 0 204 542 6958
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d1.22
X-RAY DIFFRACTIONc_mcbond_it3.531.5
X-RAY DIFFRACTIONc_mcangle_it4.682
X-RAY DIFFRACTIONc_scbond_it5.392
X-RAY DIFFRACTIONc_scangle_it7.112.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 1008 10.4 %
Rwork0.283 8709 -
obs--98.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5PHB_FAD_PYS.PARAPHB_FAD_PYS.TOPH

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