3hhl

Crystal structure of methylated RPA0582 protein

Method: X-RAY DIFFRACTION

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

RPA0582

Rhodopseudomonas palustris

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 2 CHLORIDE ION × 2 DI(HYDROXYETHYL)ETHER × 3 TRIETHYLENE GLYCOL × 1 NONAETHYLENE GLYCOL × 2 GLYCEROL × 2 TETRAETHYLENE GLYCOL × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 1 CHLORIDE ION × 2 DI(HYDROXYETHYL)ETHER × 4 TRIETHYLENE GLYCOL × 2 GLYCEROL × 2 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL × 2 PENTAETHYLENE GLYCOL × 1 TETRAETHYLENE GLYCOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6NC90_RHOPA
Isoform	—
PDB entities	1, 2, 3, 4
Chains and sequence ranges	Author chain A； PDBConstruct 2–143； UniProt 1–142 Author chain B； PDBConstruct 2–143； UniProt 1–142 Author chain C； PDBConstruct 2–143； UniProt 1–142 Author chain D； PDBConstruct 2–143； UniProt 1–142

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	3hhl
Deposition date deposition_date	2009-05-15
Structure title title	Crystal structure of methylated RPA0582 protein
Keywords keywords	;ALPHA-BETA-BARREL, STRUCTURAL GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, REDUCTIVE METHYLATION, Midwest Center for Structural Genomics, MCSG, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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.

3hhl__assembly_1__model_1

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

Download this curve (.dat)

3hhl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3hhl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.54 Å
Rg (electron density)	19.33 Å
Total Rg	20.15 Å
Atom count	2272
Residues	257
Excluded volume	40523 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3hhl__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3hhl__assembly_2__model_1`	dimeric （2）	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 (14)

Entity 1 Entity 1 polymer

Description description	RPA0582
Molecular weight formula_weight	16333.9 kDa
Mutation mutation	F61S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4944

GMTGHIDPTKEVFAQFRANDREGPIHMLNLVRLRPRAAYPDGRETTGAEAYAAYGRDSGPVSERLGGKVVWQGQFELMLIGPQDEHWDHVFIAEYPSVAAFVEMIRDPVYREAVKHRQAAVEDSRLIRLKPLKPGKGFGEIPT

Source Source

Source organism organism	Rhodopseudomonas palustris
NCBI taxonomy ID ncbi_taxonomy_id	1076
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	RPA0582
Molecular weight formula_weight	16306.9 kDa
Mutation mutation	F61S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GMTGHIDPTKEVFAQFRANDREGPIHMLNLVRLRPRAAYPDGRETTGAEAYAAYGRDSGPVSERLGGKVVWQGQFELMLIGPQDEHWDHVFIAEYPSVAAFVEMIRDPVYREAVKHRQAAVEDSRLIRLKPLKPGKGFGEIPT

Source Source

Source organism organism	Rhodopseudomonas palustris
NCBI taxonomy ID ncbi_taxonomy_id	1076
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	RPA0582
Molecular weight formula_weight	16347.0 kDa
Mutation mutation	F61S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GMTGHIDPTKEVFAQFRANDREGPIHMLNLVRLRPRAAYPDGRETTGAEAYAAYGRDSGPVSERLGGKVVWQGQFELMLIGPQDEHWDHVFIAEYPSVAAFVEMIRDPVYREAVKHRQAAVEDSRLIRLKPLKPGKGFGEIPT

Source Source

Source organism organism	Rhodopseudomonas palustris
NCBI taxonomy ID ncbi_taxonomy_id	1076
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	RPA0582
Molecular weight formula_weight	16320.9 kDa
Mutation mutation	F61S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

GMTGHIDPTKEVFAQFRANDREGPIHMLNLVRLRPRAAYPDGRETTGAEAYAAYGRDSGPVSERLGGKVVWQGQFELMLIGPQDEHWDHVFIAEYPSVAAFVEMIRDPVYREAVKHRQAAVEDSRLIRLKPLKPGKGFGEIPT

Source Source

Source organism organism	Rhodopseudomonas palustris
NCBI taxonomy ID ncbi_taxonomy_id	1076
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 8 Entity 8 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 9 Entity 9 non-polymer

Description description	NONAETHYLENE GLYCOL
Molecular weight formula_weight	414.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 11 Entity 11 non-polymer

Description description	3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
Molecular weight formula_weight	370.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 12 Entity 12 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 13 Entity 13 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 14 Entity 14 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	251

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3hhlA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	3hhlB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	3hhlC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

Domain ID domain_id	3hhlD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	100 —

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Unit-cell length a length_a	193.012 Å
Unit-cell length b length_b	193.012 Å
Unit-cell length c length_c	117.965 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	9

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.650 Å
Low-resolution limit resolution_low	32.170 Å
R factor r_factor	0.1800
R_work r_work	0.1780
R_free r_free	0.2060

Crystal structure of methylated RPA0582 protein

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

RPA0582

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

3hhl__assembly_1__model_1

3hhl__assembly_1__model_1 | I(q)

3hhl__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 (14)

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 polymer

Polymer Polymer

Source Source

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 non-polymer

Entity 12 Entity 12 non-polymer

Entity 13 Entity 13 non-polymer

Entity 14 Entity 14 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)