SAXSdb — 2r5v

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

PCZA361.1

Amycolatopsis orientalis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	COBALT (II) ION × 1 (2S)-hydroxy(4-hydroxyphenyl)ethanoic acid × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	COBALT (II) ION × 1 (2S)-hydroxy(4-hydroxyphenyl)ethanoic acid × 1 PHOSPHATE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O52791_AMYOR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–357； UniProt 1–357 Author chain B； PDBConstruct 1–357； UniProt 1–357

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	2r5v
Deposition date deposition_date	2007-09-04
Structure title title	Hydroxymandelate Synthase Crystal Structure
Keywords keywords	dioxygenase, non-heme iron, vancomycin, 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.

2r5v__assembly_1__model_1

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

Download this curve (.dat)

2r5v__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2r5v__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.82 Å
Rg (electron density)	19.42 Å
Total Rg	20.32 Å
Atom count	2598
Residues	346
Excluded volume	45542 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2r5v__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2r5v__assembly_2__model_1`	monomeric （1）	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 (5)

Entity 1 Entity 1 polymer

Description description	PCZA361.1
Molecular weight formula_weight	38377.3 kDa
EC 编号 ec_number	1.13.11.46
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	5295

MQNFEIDYVEMYVENLEVAAFSWVDKYAFAVAGTSRSADHRSIALRQGQVTLVLTEPTSDRHPAAAYLQTHGDGVADIAMATSDVAAAYEAAVRAGAEAVRAPGQHSEAAVTTATIGGFGDVVHTLIQRDGTSAELPPGFTGSMDVTNHGKGDVDLLGIDHFAICLNAGDLGPTVEYYERALGFRQIFDEHIVVGAQAMNSTVVQSASGAVTLTLIEPDRNADPGQIDEFLKDHQGAGVQHIAFNSNDAVRAVKALSERGVEFLKTPGAYYDLLGERITLQTHSLDDLRATNVLADEDHGGQLFQIFTASTHPRHTIFFEVIERQGAGTFGSSNIKALYEAVELERTGQSEFGAARR

Source Source

Source organism organism	Amycolatopsis orientalis
NCBI taxonomy ID ncbi_taxonomy_id	31958
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	COBALT (II) ION
Molecular weight formula_weight	58.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	(2S)-hydroxy(4-hydroxyphenyl)ethanoic acid
Molecular weight formula_weight	168.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	217

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2r5vA01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
Homologous superfamily homologous superfamily	10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1

Domain ID domain_id	2r5vA02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
Homologous superfamily homologous superfamily	10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1

Domain ID domain_id	2r5vB01
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
Homologous superfamily homologous superfamily	10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1

Domain ID domain_id	2r5vB02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	180 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1
Homologous superfamily homologous superfamily	10 — 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1

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Unit-cell length a length_a	106.369 Å
Unit-cell length b length_b	106.369 Å
Unit-cell length c length_c	75.951 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 41
Space-group number int_tables_number	76
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	47.570 Å
R factor r_factor	0.1770
R_work r_work	0.1740
R_free r_free	0.2270

Hydroxymandelate Synthase Crystal Structure

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

PCZA361.1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2r5v__assembly_1__model_1

2r5v__assembly_1__model_1 | I(q)

2r5v__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Hydroxymandelate Synthase Crystal Structure

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

PCZA361.1

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

2r5v__assembly_1__model_1

2r5v__assembly_1__model_1 | I(q)

2r5v__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)