3u52

X-ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase from Pseudomonas sp. OX1

Method: X-RAY DIFFRACTION

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

Phenol hydroxylase component phN

Pseudomonas stutzeri

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Phenol hydroxylase component phL × 2 （Q84AQ4） Phenol hydroxylase component phO × 2 （Q84AQ1） FE (III) ION × 4 ZINC ION × 2 COPPER (II) ION × 2 GLYCEROL × 10 XENON × 24 3[N-MORPHOLINO]PROPANE SULFONIC ACID × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q84AQ2_PSEST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–511； UniProt 1–511 Author chain B； PDBConstruct 1–511； UniProt 1–511

Phenol hydroxylase component phL

Pseudomonas stutzeri

UniProt Q84AQ4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Phenol hydroxylase component phN × 2 （Q84AQ2） Phenol hydroxylase component phO × 2 （Q84AQ1） FE (III) ION × 4 ZINC ION × 2 COPPER (II) ION × 2 GLYCEROL × 10 XENON × 24 3[N-MORPHOLINO]PROPANE SULFONIC ACID × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q84AQ4_PSEST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–333； UniProt 1–333 Author chain D； PDBConstruct 1–333； UniProt 1–333

Phenol hydroxylase component phO

Pseudomonas stutzeri

UniProt Q84AQ1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Phenol hydroxylase component phN × 2 （Q84AQ2） Phenol hydroxylase component phL × 2 （Q84AQ4） FE (III) ION × 4 ZINC ION × 2 COPPER (II) ION × 2 GLYCEROL × 10 XENON × 24 3[N-MORPHOLINO]PROPANE SULFONIC ACID × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q84AQ1_PSEST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–119； UniProt 1–119 Author chain F； PDBConstruct 1–119； UniProt 1–119

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3u52
Deposition date deposition_date	2011-10-10
Structure title title	X-ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase from Pseudomonas sp. OX1
Keywords keywords	4-Helix Bundle, Hydroxylase, Dioxygen, Hydrocarbons, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3u52__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3u52__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3u52__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	41.50 Å
Rg (electron density)	41.30 Å
Total Rg	41.44 Å
Atom count	15451
Residues	1869
Excluded volume	273880 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3u52__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Description description	Phenol hydroxylase component phN
Molecular weight formula_weight	60217.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	16039

MVSKNKKLNLKDKYQYLTRDMAWEPTYQDKKDIFPEEDFEGIKITDWSQWEDPFRLTMDAYWKYQAEKEKKLYAIFDAFAQNNGHQNISDARYVNALKLFISGISPLEHAAFQGYSKVGRQFSGAGARVACQMQAIDELRHSQTQQHAMSHYNKHFNGLHDGPHMHDRVWYLSVPKSFFDDARSAGPFEFLTAISFSFEYVLTNLLFVPFMSGAAYNGDMATVTFGFSAQSDEARHMTLGLEVIKFILEQHEDNVPIVQRWIDKWFWRGFRLLSLVSMMMDYMLPNKVMSWSEAWEVYYEQNGGALFKDLERYGIRPPKYQDVANDAKHHLSHQLWTTFYQYCQATNFHTWIPEKEEMDWMSEKYPDTFDKYYRPRYEYLAKEAAAGRRFYNNTLPQLCQVCQIPTIFTEKDAPTMLSHRQIEHEGERYHFCSDGCCDIFKHEPEKYIQAWLPVHQIYQGNCEGGDLETVVQKYYHINIGEDNFDYVGSPDQKHWLSIKGRKPADKNQDAA

Source Source

Source organism organism	Pseudomonas stutzeri
NCBI taxonomy ID ncbi_taxonomy_id	316
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Phenol hydroxylase component phL
Molecular weight formula_weight	38458.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MSIEIKTNSVEPIRHTYGHIARRFGDKPATRYQEASYDIEAKTNFHYRPQWDSEHTLNDPTRTAIRMEDWCAVSDPRQFYYGAYVGNRAKMQESAETSFGFCEKRNLLTRLSEETQKQLLRLLVPLRHVELGANMNNAKIAGDATATTVSQMHIYTGMDRLGIGQYLSRIALMIDGSTGAALDESKAYWMDDEMWQPMRKLVEDTLVVDDWFELTLVQNILIDGMMYPLVYDKMDQWFESQGAEDVSMLTEFMRDWYKESLRWTNAMMKAVAGESETNRELLQKWIDHWEPQAYEALKPLAEASVGIDGLNEARAELSARLKKFELQSRGVSA

Source Source

Source organism organism	Pseudomonas stutzeri
NCBI taxonomy ID ncbi_taxonomy_id	316
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Phenol hydroxylase component phO
Molecular weight formula_weight	13248.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

MSVNALYDYKFEPKDKVENFHGMQLLYVYWPDHLLFCAPFALLVQPGMTFSALVDEILKPATAAHPDSAKADFLNAEWLLNDEPFTPKADASLKEQGIDHKSMLTVTTPGLKGMANAGY

Source Source

Source organism organism	Pseudomonas stutzeri
NCBI taxonomy ID ncbi_taxonomy_id	316
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	FE (III) ION
Molecular weight formula_weight	55.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 8 Entity 8 non-polymer

Description description	XENON
Molecular weight formula_weight	131.3 kDa
Source method src_method	syn
Copy count entity_count	24

Entity 9 Entity 9 non-polymer

Description description	3[N-MORPHOLINO]PROPANE SULFONIC ACID
Molecular weight formula_weight	209.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	588

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	3u52A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	620 — Ribonucleotide Reductase, subunit A
Homologous superfamily homologous superfamily	20 — Ribonucleotide Reductase, subunit A

Domain ID domain_id	3u52B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	620 — Ribonucleotide Reductase, subunit A
Homologous superfamily homologous superfamily	20 — Ribonucleotide Reductase, subunit A

Domain ID domain_id	3u52C00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	620 — Ribonucleotide Reductase, subunit A
Homologous superfamily homologous superfamily	20 — Ribonucleotide Reductase, subunit A

Domain ID domain_id	3u52D00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	620 — Ribonucleotide Reductase, subunit A
Homologous superfamily homologous superfamily	20 — Ribonucleotide Reductase, subunit A

Domain ID domain_id	3u52E01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	560 — Phenol hydroxylase

Domain ID domain_id	3u52F01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	560 — Phenol hydroxylase

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Unit-cell length a length_a	83.942 Å
Unit-cell length b length_b	141.761 Å
Unit-cell length c length_c	181.207 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	1.950 Å
Low-resolution limit resolution_low	38.000 Å
R factor r_factor	0.1852
R_work r_work	0.1830
R_free r_free	0.2277

X-ray Crystal Structure of Xenon-Pressurized Phenol Hydroxylase from Pseudomonas sp. OX1

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

Phenol hydroxylase component phN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Phenol hydroxylase component phL

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Phenol hydroxylase component phO

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3u52__assembly_1__model_1

3u52__assembly_1__model_1 | I(q)

3u52__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (2)