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- PDB-1k0j: Pseudomonas aeruginosa phbh R220Q in complex with NADPH and free ... -

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Basic information

Entry
Database: PDB / ID: 1k0j
TitlePseudomonas aeruginosa phbh R220Q in complex with NADPH and free of p-OHB
ComponentsP-HYDROXYBENZOATE HYDROXYLASE
KeywordsHYDROLASE / phbh / FAD / NADPH
Function / homology
Function and homology information


4-hydroxybenzoate 3-monooxygenase / 4-hydroxybenzoate 3-monooxygenase [NADPH] activity / 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 / Chem-NDP / p-hydroxybenzoate hydroxylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWang, J. / Ortiz-Maldonado, M. / Entsch, B. / Ballou, D. / Gatti, D.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Protein and ligand dynamics in 4-hydroxybenzoate hydroxylase.
Authors: Wang, J. / Ortiz-Maldonado, M. / Entsch, B. / Massey, V. / Ballou, D. / Gatti, D.L.
History
DepositionSep 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 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 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3658
Polymers44,3531
Non-polymers2,0117
Water2,090116
1
A: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules

A: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,73016
Polymers88,7072
Non-polymers4,02314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_757-x+2,y,-z+5/21
Buried area8670 Å2
ΔGint-142 kcal/mol
Surface area31470 Å2
MethodPISA
2
A: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules

A: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,73016
Polymers88,7072
Non-polymers4,02314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_567x,-y+1,-z+21
Buried area9320 Å2
ΔGint-142 kcal/mol
Surface area30820 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)71.845, 139.146, 91.637
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
DetailsThe enzyme is a dimer in solution. But only one monomer is present in the asymmetric unit.

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Components

#1: Protein P-HYDROXYBENZOATE HYDROXYLASE


Mass: 44353.484 Da / Num. of mol.: 1 / Mutation: R220Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: bl21 / Production host: Escherichia coli (E. coli)
References: UniProt: P20586, 4-hydroxybenzoate 3-monooxygenase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.58 Å3/Da / Density % sol: 52.34 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM potassium phosphate, 0.05 mM glutathion, 30mM sodium sulfite 0.02mM FAD, 450mM ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 303K
Crystal grow
*PLUS
Temperature: 30 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14 mg/mlprotein1drop
2100 mMKPi1droppH7.0
30.05 mMglutathione1drop
430 mMsodium solfite1drop
50.02 mMFAD1drop
6450 mMammonium sulfate1drop
7900 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 5, 2001 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→22.07 Å / Num. all: 19340 / Num. obs: 19340 / % possible obs: 81.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.8 % / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.13
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.726 / Num. unique all: 2016 / % possible all: 57.3
Reflection
*PLUS
Num. obs: 20552 / % possible obs: 86.6 % / Num. measured all: 262880 / Rmerge(I) obs: 0.13

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Processing

Software
NameClassification
CNSrefinement
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→22.07 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1906 -RANDOM
Rwork0.222 ---
all-19340 --
obs-19340 86.6 %-
Displacement parametersBiso mean: 42.5 Å2
Baniso -1Baniso -2Baniso -3
1-28.5 Å20 Å20 Å2
2---13.45 Å20 Å2
3----15.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.67 Å
Refinement stepCycle: LAST / Resolution: 2.2→22.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3123 0 126 116 3365
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.88
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 22 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 42.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.88

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