1dii

CRYSTAL STRUCTURE OF P-CRESOL METHYLHYDROXYLASE AT 2.5 A RESOLUTION

Method: X-RAY DIFFRACTION D_max: 102.6 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

P-CRESOL METHYLHYDROXYLASE

OrganismNot specified

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–521 Chain B； UniProt 1–521	Fragment：FLAVOPROTEIN SUBUNIT	P-CRESOL METHYLHYDROXYLASE × 2 （P09787） CL CHLORIDE ION × 2 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 HEC HEME C × 2	X-RAY DIFFRACTION X-ray crystallization conditions：LIQUID DIFFUSION；pH 7；298 K；PEG 8000, NA/K PHOSPHATE, NACL, pH 7.0, LIQUID DIFFUSION, temperature 298K	Resolution 2.50 Å R-free 0.230

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 1DII	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DIQ CRYSTAL STRUCTURE OF P-CRESOL METHYLHYDROXYLASE WITH SUBSTRATE BOUND Deposited 1999-11-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–521（521 aa） Fragment：FLAVOPROTEIN SUBUNIT Chain B 1–521（521 aa） Fragment：FLAVOPROTEIN SUBUNIT	Not recorded	CL CHLORIDE ION × 2 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 PCR P-CRESOL × 2 HEC HEME C × 2	X-RAY DIFFRACTION X-ray crystallization conditions LIQUID DIFFUSION；pH 7；298 K；PEG 8000, Na/K phosphate, NaCl, Crystals soaked with substrate p-cresol , pH 7.0, LIQUID DIFFUSION, temperature 298K	Resolution 2.75 Å R-free 0.183
1WVE p-Cresol Methylhydroxylase: Alteration of the Structure of the Flavoprotein Subunit upon its Binding to the Cytochrome Subunit Deposited 2004-12-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–520（520 aa） Chain B 1–520（520 aa）	Not recorded	CL CHLORIDE ION × 2 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 4 ACY ACETIC ACID × 4 HEM PROTOPORPHYRIN IX CONTAINING FE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；296 K；PEG 8000, Tris, ammonium acetate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K	Resolution 1.85 Å R-free 0.194
1WVF p-Cresol Methylhydroxylase: Alteration of the Structure of the Flavoprotein Subunit upon its Binding to the Cytochrome Subunit Deposited 2004-12-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–520（520 aa）	Not recorded	CL CHLORIDE ION × 2 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 ACY ACETIC ACID × 4 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；296 K；PEG 1500, acetate, magnesium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K	Resolution 1.30 Å R-free 0.167

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DH4C_PSEPU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–521； UniProt 1–521 Author chain B； PDBConstruct 1–521； UniProt 1–521

P-CRESOL METHYLHYDROXYLASE

OrganismNot specified

UniProt P09787

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 34–113 Chain D； UniProt 34–113	Fragment：CYTOCHROME SUBUNIT	P-CRESOL METHYLHYDROXYLASE × 2 （P09788） CL CHLORIDE ION × 2 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 HEC HEME C × 2	X-RAY DIFFRACTION X-ray crystallization conditions：LIQUID DIFFUSION；pH 7；298 K；PEG 8000, NA/K PHOSPHATE, NACL, pH 7.0, LIQUID DIFFUSION, temperature 298K	Resolution 2.50 Å R-free 0.230

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 1DII	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1DIQ CRYSTAL STRUCTURE OF P-CRESOL METHYLHYDROXYLASE WITH SUBSTRATE BOUND Deposited 1999-11-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 34–113（80 aa） Fragment：CYTOCHROME SUBUNIT Chain D 34–113（80 aa） Fragment：CYTOCHROME SUBUNIT	Not recorded	CL CHLORIDE ION × 2 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 PCR P-CRESOL × 2 HEC HEME C × 2	X-RAY DIFFRACTION X-ray crystallization conditions LIQUID DIFFUSION；pH 7；298 K；PEG 8000, Na/K phosphate, NaCl, Crystals soaked with substrate p-cresol , pH 7.0, LIQUID DIFFUSION, temperature 298K	Resolution 2.75 Å R-free 0.183
1WVE p-Cresol Methylhydroxylase: Alteration of the Structure of the Flavoprotein Subunit upon its Binding to the Cytochrome Subunit Deposited 2004-12-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 34–113（80 aa） Chain D 34–113（80 aa）	Not recorded	CL CHLORIDE ION × 2 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 4 ACY ACETIC ACID × 4 HEM PROTOPORPHYRIN IX CONTAINING FE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；296 K；PEG 8000, Tris, ammonium acetate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K	Resolution 1.85 Å R-free 0.194

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CY4C_PSEPU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–80； UniProt 34–113 Author chain D； PDBConstruct 1–80； UniProt 34–113

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1dii
Deposition date deposition_date	1999-11-29
Structure title title	CRYSTAL STRUCTURE OF P-CRESOL METHYLHYDROXYLASE AT 2.5 A RESOLUTION
Keywords keywords	FLAVOCYTOCHROME, ELECTRON-TRANSFER, FAD, HEME, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	31.81 Å
Radius of gyration Rg (electron density) rg_electron	30.99 Å
Forward intensity I(0) i0	275246000.00
Molecular weight molecular_weight	133220.0 kDa
Excluded volume excluded_volume	166370 Å³
Envelope volume envelope_volume	195080 Å³
Hydration-shell volume shell_volume	50307 Å³
Envelope diameter envelope_diameter	106.2 Å
Shell Rg shell_rg	39.98 Å
Envelope Rg envelope_rg	31.24 Å
Shape Rg shape_rg	31.00 Å
Total Rg total_rg	31.62 Å
Total atoms total_atoms	9362
Residues n_residues	1176
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	102.6 Å
Rg (real space) rg_real	31.71 Å
Rg uncertainty (real space) rg_real_error	0.61 Å
I(0) (real space) i0_real	2.7520e+08
I(0) uncertainty (real space) i0_real_error	4.3680e+06
Rg (reciprocal space) rg_reciprocal	31.76 Å
I(0) (reciprocal space) i0_reciprocal	275300000.0000
Solution quality estimate total_estimate	0.8918
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	36.9 Å
Skewness Skewness skewness	0.295
Kurtosis Kurtosis kurtosis	-0.392
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	140200000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.877; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.963

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	P-CRESOL METHYLHYDROXYLASE
Molecular weight formula_weight	58006.0 kDa
EC 编号 ec_number	1.17.99.1
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	9805

MSEQNNAVLPKGVTQGEFNKAVQKFRALLGDDNVLVESDQLVPYNKIMMPVENAAHAPSAAVTATTVEQVQGVVKICNEHKIPIWTISTGRNFGYGSAAPVQRGQVILDLKKMNKIIKIDPEMCYALVEPGVTFGQMYDYIQENNLPVMLSFSAPSAIAGPVGNTMDRGVGYTPYGEHFMMQCGMEVVLANGDVYRTGMGGVPGSNTWQIFKWGYGPTLDGMFTQANYGICTKMGFWLMPKPPVFKPFEVIFEDEADIVEIVDALRPLRMSNTIPNSVVIASTLWEAGSAHLTRAQYTTEPGHTPDSVIKQMQKDTGMGAWNLYAALYGTQEQVDVNWKIVTDVFKKLGKGRIVTQEEAGDTQPFKYRAQLMSGVPNLQEFGLYNWRGGGGSMWFAPVSEARGSECKKQAAMAKRVLHKYGLDYVAEFIVAPRDMHHVIDVLYDRTNPEETKRADACFNELLDEFEKEGYAVYRVNTRFQDRVAQSYGPVKRKLEHAIKRAVDPNNILAPGRSGIDLNNDF

Entity 2 Entity 2 polymer

Description description	P-CRESOL METHYLHYDROXYLASE
Molecular weight formula_weight	8611.6 kDa
EC 编号 ec_number	1.17.99.1
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

DSQWGSGKNLYDKVCGHCHKPEVGVGPVLEGRGLPEAYIKDIVRNGFRAMPAFPASYVDDESLTQVAEYLSSLPAPAAQP

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	HEME C
Molecular weight formula_weight	618.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	385

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1diia1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.32 — FAD-linked oxidases, C-terminal domain
Family Family family	d.58.32.1 — Vanillyl-alcohol oxidase-like

Domain ID domain_id	d1diia2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.145 — FAD-binding/transporter-associated domain-like
Superfamily Superfamily superfamily	d.145.1 — FAD-binding/transporter-associated domain-like
Family Family family	d.145.1.1 — FAD-linked oxidases, N-terminal domain

Domain ID domain_id	d1diib1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.32 — FAD-linked oxidases, C-terminal domain
Family Family family	d.58.32.1 — Vanillyl-alcohol oxidase-like

Domain ID domain_id	d1diib2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.145 — FAD-binding/transporter-associated domain-like
Superfamily Superfamily superfamily	d.145.1 — FAD-binding/transporter-associated domain-like
Family Family family	d.145.1.1 — FAD-linked oxidases, N-terminal domain

Domain ID domain_id	d1diic_
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.1 — monodomain cytochrome c

Domain ID domain_id	d1diid_
Class class	a — All alpha proteins
Fold Fold fold	a.3 — Cytochrome c
Superfamily Superfamily superfamily	a.3.1 — Cytochrome c
Family Family family	a.3.1.1 — monodomain cytochrome c

CATH v4.4 (10 domains)

Domain ID domain_id	1diiA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	462 — Vanillyl-alcohol Oxidase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — FAD-linked oxidases, C-terminal domain

Domain ID domain_id	1diiA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2

Domain ID domain_id	1diiA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1diiA04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	45 — Vanillyl-alcohol Oxidase; Chain A, domain 4
Homologous superfamily homologous superfamily	10 — Vanillyl-alcohol Oxidase; Chain A, domain 4

Domain ID domain_id	1diiB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	462 — Vanillyl-alcohol Oxidase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — FAD-linked oxidases, C-terminal domain

Domain ID domain_id	1diiB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2

Domain ID domain_id	1diiB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1diiB04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	45 — Vanillyl-alcohol Oxidase; Chain A, domain 4
Homologous superfamily homologous superfamily	10 — Vanillyl-alcohol Oxidase; Chain A, domain 4

Domain ID domain_id	1diiC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

Domain ID domain_id	1diiD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	760 — Cytochrome Bc1 Complex; Chain D, domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome c-like domain

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8. Citations (2)

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Unit-cell length a length_a	140.300 Å
Unit-cell length b length_b	130.600 Å
Unit-cell length c length_c	74.100 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1720
R_work r_work	0.1720
R_free r_free	0.2300

fit	/app/data/saxs_computation/di/1dii/1dii.fit
pddf	/app/data/pr_computation/di/1dii/1dii.pr.out
profile	/app/data/saxs_computation/di/1dii/1dii.dat

CRYSTAL STRUCTURE OF P-CRESOL METHYLHYDROXYLASE AT 2.5 A RESOLUTION

1. Protein Identity and Related Structures Protein Identity & Related Structures

P-CRESOL METHYLHYDROXYLASE

State in the Current Structure

Other States of the Same Protein in the Database

P-CRESOL METHYLHYDROXYLASE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (6 domains)

CATH v4.4 (10 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)