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- PDB-1k0i: Pseudomonas aeruginosa phbh R220Q in complex with 100mM PHB -

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Basic information

Entry
Database: PDB / ID: 1k0i
TitlePseudomonas aeruginosa phbh R220Q in complex with 100mM PHB
ComponentsP-HYDROXYBENZOATE HYDROXYLASE
KeywordsHYDROLASE / phbh / FAD / p-OHB
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 ...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 / SULFITE ION / p-hydroxybenzoate hydroxylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / 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 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)46,26413
Polymers44,3531
Non-polymers1,91012
Water4,612256
1
A: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules

A: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,52826
Polymers88,7072
Non-polymers3,82124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_757-x+2,y,-z+5/21
Buried area5850 Å2
ΔGint-181 kcal/mol
Surface area33580 Å2
MethodPISA
2
A: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules

A: P-HYDROXYBENZOATE HYDROXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,52826
Polymers88,7072
Non-polymers3,82124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_567x,-y+1,-z+21
Buried area6520 Å2
ΔGint-157 kcal/mol
Surface area32540 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.678, 138.150, 92.509
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-708-

SO4

DetailsThe enzyme is a dimer in solution. But only one monomer is present in the asymmetric unit

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 268 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical ChemComp-PHB / P-HYDROXYBENZOIC ACID


Mass: 138.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 51.66 %
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 20, 2001 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→22.02 Å / Num. all: 38363 / Num. obs: 38363 / % possible obs: 90.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.081
Reflection shellResolution: 1.8→1.91 Å / Rmerge(I) obs: 0.471 / Num. unique all: 3306 / % possible all: 53
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 22 Å / Num. measured all: 557623

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Processing

Software
NameVersionClassification
CNS1refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IUW

1iuw


Resolution: 1.8→22.02 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 3851 -random
Rwork0.207 ---
all-38363 --
obs-38363 90.6 %-
Displacement parametersBiso mean: 31.9 Å2
Baniso -1Baniso -2Baniso -3
1-6.31 Å20 Å20 Å2
2---2.43 Å20 Å2
3----3.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 1.8→22.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3123 0 117 256 3496
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.83
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 22 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.207 / Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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