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1k0j

Pseudomonas aeruginosa phbh R220Q in complex with NADPH and free of p-OHB

Method: X-RAY DIFFRACTION Dmax: 73.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

P-HYDROXYBENZOATE HYDROXYLASE

Pseudomonas aeruginosa

UniProt P20586

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–394 Mutation：R220Q SO4 SULFATE ION × 10 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；303 K；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 Resolution 2.20 Å R-free 0.275
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–394 Mutation：R220Q SO4 SULFATE ION × 10 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 NDP NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；303 K；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 Resolution 2.20 Å R-free 0.275

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1K0J Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1D7L STRUCTURE-FUNCTION CORRELATIONS OF THE REACTION OF REDUCED NICOTINAMIDE ANALOGS WITH P-HYDROXYBENZOATE HYDROXYLASE SUBSTITUTED WITH A SERIES OF 8-SUBSTITUTED FLAVINS Deposited 1999-10-18 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–394（394 aa）
Not recorded SO4 SULFATE ION × 3 RFL 8-DEMETHYL-8-DIMETHYLAMINO-FLAVIN-ADENINE-DINUCLEOTIDE × 1 PHB P-HYDROXYBENZOIC ACID × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å R-free 0.235
1D7L STRUCTURE-FUNCTION CORRELATIONS OF THE REACTION OF REDUCED NICOTINAMIDE ANALOGS WITH P-HYDROXYBENZOATE HYDROXYLASE SUBSTITUTED WITH A SERIES OF 8-SUBSTITUTED FLAVINS Deposited 1999-10-18 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–394（394 aa）
Not recorded SO4 SULFATE ION × 6 RFL 8-DEMETHYL-8-DIMETHYLAMINO-FLAVIN-ADENINE-DINUCLEOTIDE × 2 PHB P-HYDROXYBENZOIC ACID × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å R-free 0.235
1DOB THE MOBIL FLAVIN OF 4-OH BENZOATE HYDROXYLASE: MOTION OF A PROSTHETIC GROUP REGULATES CATALYSIS Deposited 1994-09-06 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–394（394 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 PHB P-HYDROXYBENZOIC ACID × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
1DOC THE MOBIL FLAVIN OF 4-OH BENZOATE HYDROXYLASE: MOTION OF A PROSTHETIC GROUP REGULATES CATALYSIS Deposited 1994-09-06 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–394（394 aa）
Not recorded BR BROMIDE ION × 6 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 PHB P-HYDROXYBENZOIC ACID × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
1DOD THE MOBIL FLAVIN OF 4-OH BENZOATE HYDROXYLASE: MOTION OF A PROSTHETIC GROUP REGULATES CATALYSIS Deposited 1994-09-06 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–394（394 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 DOB 2,4-DIHYDROXYBENZOIC ACID × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å
1DOE THE MOBIL FLAVIN OF 4-OH BENZOATE HYDROXYLASE: MOTION OF A PROSTHETIC GROUP REGULATES CATALYSIS Deposited 1994-09-06 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–394（394 aa）
Not recorded BR BROMIDE ION × 4 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 DOB 2,4-DIHYDROXYBENZOIC ACID × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å
1IUS P-HYDROXYBENZOATE HYDROXYLASE COMPLEXED WITH 4-AMINOBENZOATE AT PH 5.0 Deposited 1995-11-22 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–394（394 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 PAB 4-AMINOBENZOIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5；pH 5.0
Resolution 2.20 Å
1IUT P-HYDROXYBENZOATE HYDROXYLASE COMPLEXED WITH 4-AMINOBENZOATE AT PH 7.4 Deposited 1995-11-22 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–394（394 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 PAB 4-AMINOBENZOIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；pH 7.4
Resolution 2.00 Å
1IUU P-HYDROXYBENZOATE HYDROXYLASE COMPLEXED WITH 4-AMINOBENZOATE AT PH 9.4 Deposited 1995-11-22 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–394（394 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 PAB 4-AMINOBENZOIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9.4；pH 9.4
Resolution 2.00 Å
1IUV P-HYDROXYBENZOATE HYDROXYLASE COMPLEXED WITH 4-4-HYDROXYBENZOATE AT PH 5.0 Deposited 1995-11-22 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–394（394 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 PHB P-HYDROXYBENZOIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5；pH 5.0
Resolution 2.50 Å
1IUW P-HYDROXYBENZOATE HYDROXYLASE COMPLEXED WITH 4-4-HYDROXYBENZOATE AT PH 7.4 Deposited 1995-11-22 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–394（394 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 PHB P-HYDROXYBENZOIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；pH 7.4
Resolution 2.00 Å
1IUX P-HYDROXYBENZOATE HYDROXYLASE COMPLEXED WITH 4-4-HYDROXYBENZOATE AT PH 9.4 Deposited 1995-11-22 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–394（394 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 PHB P-HYDROXYBENZOIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 9.4；pH 9.4
Resolution 2.00 Å
1K0I Pseudomonas aeruginosa phbh R220Q in complex with 100mM PHB Deposited 2001-09-19 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–394（394 aa）
Mutation：R220Q SO4 SULFATE ION × 16 SO3 SULFITE ION × 2 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 PHB P-HYDROXYBENZOIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；303 K；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
Resolution 1.80 Å R-free 0.240
1K0I Pseudomonas aeruginosa phbh R220Q in complex with 100mM PHB Deposited 2001-09-19 Different ligand/ion Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–394（394 aa）
Mutation：R220Q SO4 SULFATE ION × 16 SO3 SULFITE ION × 2 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 PHB P-HYDROXYBENZOIC ACID × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；303 K；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
Resolution 1.80 Å R-free 0.240
1K0L Pseudomonas aeruginosa phbh R220Q free of p-OHB Deposited 2001-09-19 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–394（394 aa）
Mutation：R220Q SO4 SULFATE ION × 16 SO3 SULFITE ION × 4 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；303 K；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
Resolution 2.00 Å R-free 0.247
1K0L Pseudomonas aeruginosa phbh R220Q free of p-OHB Deposited 2001-09-19 Different ligand/ion Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–394（394 aa）
Mutation：R220Q SO4 SULFATE ION × 16 SO3 SULFITE ION × 4 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；303 K；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
Resolution 2.00 Å R-free 0.247
1PXA CRYSTAL STRUCTURES OF MUTANT PSEUDOMONAS AERUGINOSA P-HYDROXYBENZOATE HYDROXYLASE: THE TYR201PHE, TYR385PHE, AND ASN300ASP VARIANTS Deposited 1994-09-27 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–394（394 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 PHB P-HYDROXYBENZOIC ACID × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å
1PXB CRYSTAL STRUCTURES OF MUTANT PSEUDOMONAS AERUGINOSA P-HYDROXYBENZOATE HYDROXYLASE: THE TYR201PHE, TYR385PHE, AND ASN300ASP VARIANTS Deposited 1994-09-27 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–394（394 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 PHB P-HYDROXYBENZOIC ACID × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å
1PXC CRYSTAL STRUCTURES OF MUTANT PSEUDOMONAS AERUGINOSA P-HYDROXYBENZOATE HYDROXYLASE: THE TYR201PHE, TYR385PHE, AND ASN300ASP VARIANTS Deposited 1994-09-27 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–394（394 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 PHB P-HYDROXYBENZOIC ACID × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å
1YKJ A45G p-hydroxybenzoate hydroxylase with p-hydroxybenzoate bound Deposited 2005-01-18 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–394（394 aa）
Chain B 1–394（394 aa）
Mutation：A45G Mutation：A45G SO4 SULFATE ION × 12 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 PHB P-HYDROXYBENZOIC ACID × 2 PSL PYROSULFATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；310 K；ammonium sulfate, tris-sulfate, fad, edta, glutathion, sodium sulfite, p-hydroxybenzoate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K
Resolution 2.00 Å R-free 0.265
1YKJ A45G p-hydroxybenzoate hydroxylase with p-hydroxybenzoate bound Deposited 2005-01-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–394（394 aa）
Chain B 1–394（394 aa）
Mutation：A45G Mutation：A45G SO4 SULFATE ION × 24 FAD FLAVIN-ADENINE DINUCLEOTIDE × 4 PHB P-HYDROXYBENZOIC ACID × 4 PSL PYROSULFATE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；310 K；ammonium sulfate, tris-sulfate, fad, edta, glutathion, sodium sulfite, p-hydroxybenzoate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K
Resolution 2.00 Å R-free 0.265

17 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PHHY_PSEAE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–394； UniProt 1–394

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1k0j

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1k0j
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1k0j
Deposition date deposition_date2001-09-19
Structure title titlePseudomonas aeruginosa phbh R220Q in complex with NADPH and free of p-OHB
Keywords keywordsphbh, FAD, NADPH, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.63 Å
Radius of gyration Rg (electron density) rg_electron21.58 Å
Forward intensity I(0) i038762300.00
Molecular weight molecular_weight46303.0 kDa
Excluded volume excluded_volume57180 ų
Envelope volume envelope_volume66610 ų
Hydration-shell volume shell_volume25454 ų
Envelope diameter envelope_diameter75.9 Å
Shell Rg shell_rg28.74 Å
Envelope Rg envelope_rg21.82 Å
Shape Rg shape_rg21.58 Å
Total Rg total_rg22.41 Å
Total atoms total_atoms3249
Residues n_residues394
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax73.5 Å
Rg (real space) rg_real22.58 Å
Rg uncertainty (real space) rg_real_error0.43 Å
I(0) (real space) i0_real3.8760e+07
I(0) uncertainty (real space) i0_real_error5.2750e+05
Rg (reciprocal space) rg_reciprocal22.59 Å
I(0) (reciprocal space) i0_reciprocal38760000.0000
Solution quality estimate total_estimate0.8843
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary26.8 Å
Skewness Skewness skewness0.334
Kurtosis Kurtosis kurtosis-0.299
Angular range angular_range— – 0.3500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14770000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.838; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.978
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1k0ja1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.3 — FAD/NAD(P)-binding domain
Superfamily Superfamily superfamilyc.3.1 — FAD/NAD(P)-binding domain
Family Family familyc.3.1.2 — FAD-linked reductases, N-terminal domain
Domain ID domain_idd1k0ja2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.16 — FAD-linked reductases, C-terminal domain
Superfamily Superfamily superfamilyd.16.1 — FAD-linked reductases, C-terminal domain
Family Family familyd.16.1.2 — PHBH-like

CATH v4.4 (2 domains)

Domain ID domain_id1k0jA01
Class class3 — Alpha Beta
Architecture architecture50 — 3-Layer(bba) Sandwich
Topology topology50 — FAD/NAD(P)-binding domain
Homologous superfamily homologous superfamily60 — FAD/NAD(P)-binding domain
Domain ID domain_id1k0jA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology9 — D-Amino Acid Oxidase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — D-Amino Acid Oxidase, subunit A, domain 2
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8. Citations (1)

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9. Files and Curves (10)