3wof

Crystal structure of P23-45 gp39 (6-132) bound to Thermus thermophilus RNA polymerase beta-flap domain

Method: X-RAY DIFFRACTION

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

DNA-directed RNA polymerase subunit beta

Thermus thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Putative uncharacterized protein × 1 （A7XX65）	Consistent with protein count
10	Protein heterocomplex	Heteromer	Protein 2	Putative uncharacterized protein × 1 （A7XX65）	Consistent with protein count
11	Protein heterocomplex	Heteromer	Protein 2	Putative uncharacterized protein × 1 （A7XX65）	Consistent with protein count
12	Protein heterocomplex	Heteromer	Protein 2	Putative uncharacterized protein × 1 （A7XX65）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Putative uncharacterized protein × 1 （A7XX65）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Putative uncharacterized protein × 1 （A7XX65）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Putative uncharacterized protein × 1 （A7XX65）	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	Putative uncharacterized protein × 1 （A7XX65）	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	Putative uncharacterized protein × 1 （A7XX65）	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 2	Putative uncharacterized protein × 1 （A7XX65）	Consistent with protein count
8	Protein heterocomplex	Heteromer	Protein 2	Putative uncharacterized protein × 1 （A7XX65）	Consistent with protein count
9	Protein heterocomplex	Heteromer	Protein 2	Putative uncharacterized protein × 1 （A7XX65）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOB_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–130； UniProt 703–830 Author chain C； PDBConstruct 3–130； UniProt 703–830 Author chain E； PDBConstruct 3–130； UniProt 703–830 Author chain G； PDBConstruct 3–130； UniProt 703–830 Author chain I； PDBConstruct 3–130； UniProt 703–830 Author chain K； PDBConstruct 3–130； UniProt 703–830 Author chain M； PDBConstruct 3–130； UniProt 703–830 Author chain O； PDBConstruct 3–130； UniProt 703–830 Author chain Q； PDBConstruct 3–130； UniProt 703–830 Author chain S； PDBConstruct 3–130； UniProt 703–830 Author chain U； PDBConstruct 3–130； UniProt 703–830 Author chain W； PDBConstruct 3–130； UniProt 703–830

Putative uncharacterized protein

Thermus phage P23-45

UniProt A7XX65

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	DNA-directed RNA polymerase subunit beta × 1 （Q8RQE9）	Consistent with protein count
10	Protein heterocomplex	Heteromer	Protein 2	DNA-directed RNA polymerase subunit beta × 1 （Q8RQE9）	Consistent with protein count
11	Protein heterocomplex	Heteromer	Protein 2	DNA-directed RNA polymerase subunit beta × 1 （Q8RQE9）	Consistent with protein count
12	Protein heterocomplex	Heteromer	Protein 2	DNA-directed RNA polymerase subunit beta × 1 （Q8RQE9）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	DNA-directed RNA polymerase subunit beta × 1 （Q8RQE9）	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	DNA-directed RNA polymerase subunit beta × 1 （Q8RQE9）	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	DNA-directed RNA polymerase subunit beta × 1 （Q8RQE9）	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	DNA-directed RNA polymerase subunit beta × 1 （Q8RQE9）	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	DNA-directed RNA polymerase subunit beta × 1 （Q8RQE9）	Consistent with protein count
7	Protein heterocomplex	Heteromer	Protein 2	DNA-directed RNA polymerase subunit beta × 1 （Q8RQE9）	Consistent with protein count
8	Protein heterocomplex	Heteromer	Protein 2	DNA-directed RNA polymerase subunit beta × 1 （Q8RQE9）	Consistent with protein count
9	Protein heterocomplex	Heteromer	Protein 2	DNA-directed RNA polymerase subunit beta × 1 （Q8RQE9）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A7XX65_9CAUD
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–129； UniProt 6–132 Author chain D； PDBConstruct 3–129； UniProt 6–132 Author chain F； PDBConstruct 3–129； UniProt 6–132 Author chain H； PDBConstruct 3–129； UniProt 6–132 Author chain J； PDBConstruct 3–129； UniProt 6–132 Author chain L； PDBConstruct 3–129； UniProt 6–132 Author chain N； PDBConstruct 3–129； UniProt 6–132 Author chain P； PDBConstruct 3–129； UniProt 6–132 Author chain R； PDBConstruct 3–129； UniProt 6–132 Author chain T； PDBConstruct 3–129； UniProt 6–132 Author chain V； PDBConstruct 3–129； UniProt 6–132 Author chain X； PDBConstruct 3–129； UniProt 6–132

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	3wof
Deposition date deposition_date	2013-12-26
Structure title title	Crystal structure of P23-45 gp39 (6-132) bound to Thermus thermophilus RNA polymerase beta-flap domain
Keywords keywords	Transcription, RNA polymerase, TRANSFERASE-TRANSCRIPTION complex; TRANSFERASE/TRANSCRIPTION
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.

3wof__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3wof__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3wof__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	20.16 Å
Rg (electron density)	19.59 Å
Total Rg	20.52 Å
Atom count	1846
Residues	232
Excluded volume	32936 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3wof__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3wof__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3wof__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3wof__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3wof__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3wof__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3wof__assembly_7__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`3wof__assembly_8__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`3wof__assembly_9__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`3wof__assembly_10__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
11	1	`3wof__assembly_11__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
12	1	`3wof__assembly_12__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 (2)

Entity 1 Entity 1 polymer

Description description	DNA-directed RNA polymerase subunit beta
Molecular weight formula_weight	14481.5 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K,M,O,Q,S,U,W
Atom count atom_count	22026

GPIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEEGVVRIGAEVKPGDILVGRTSFKGESEPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQK

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Putative uncharacterized protein
Molecular weight formula_weight	14855.0 kDa
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H,J,L,N,P,R,T,V,X

GPVEPYIRLFEAIPDAETELATFYDADLDTLPPRMFLPSGDLYTPPGPVRLEEIKRKRRVRLVKVSIYRFEHVGLGLAARPYAYAYAWQGDNGILHLYHAPVVLEDVPEVLELDEVTYNESYVRLMRAM

Source Source

Source organism organism	Thermus phage P23-45
NCBI taxonomy ID ncbi_taxonomy_id	466051
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id	3wofA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	150 — RNA polymerase II, Rpb2 subunit, wall domain

Domain ID domain_id	3wofB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1250 —

Domain ID domain_id	3wofC00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	150 — RNA polymerase II, Rpb2 subunit, wall domain

Domain ID domain_id	3wofD00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1250 —

Domain ID domain_id	3wofE00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	150 — RNA polymerase II, Rpb2 subunit, wall domain

Domain ID domain_id	3wofF00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1250 —

Domain ID domain_id	3wofG00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	150 — RNA polymerase II, Rpb2 subunit, wall domain

Domain ID domain_id	3wofH00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1250 —

Domain ID domain_id	3wofI00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	150 — RNA polymerase II, Rpb2 subunit, wall domain

Domain ID domain_id	3wofJ00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1250 —

Domain ID domain_id	3wofK00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	150 — RNA polymerase II, Rpb2 subunit, wall domain

Domain ID domain_id	3wofL00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1250 —

Domain ID domain_id	3wofM00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	150 — RNA polymerase II, Rpb2 subunit, wall domain

Domain ID domain_id	3wofN00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1250 —

Domain ID domain_id	3wofO00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	150 — RNA polymerase II, Rpb2 subunit, wall domain

Domain ID domain_id	3wofP00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1250 —

Domain ID domain_id	3wofQ00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	150 — RNA polymerase II, Rpb2 subunit, wall domain

Domain ID domain_id	3wofR00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1250 —

Domain ID domain_id	3wofS00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	150 — RNA polymerase II, Rpb2 subunit, wall domain

Domain ID domain_id	3wofT00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1250 —

Domain ID domain_id	3wofU00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	150 — RNA polymerase II, Rpb2 subunit, wall domain

Domain ID domain_id	3wofV00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1250 —

Domain ID domain_id	3wofW00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	150 — RNA polymerase II, Rpb2 subunit, wall domain

Domain ID domain_id	3wofX00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	1250 —

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Unit-cell length a length_a	213.777 Å
Unit-cell length b length_b	213.777 Å
Unit-cell length c length_c	234.598 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	96

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	3.298 Å
Low-resolution limit resolution_low	34.549 Å
R factor r_factor	0.2205
R_work r_work	0.2191
R_free r_free	0.2464

Crystal structure of P23-45 gp39 (6-132) bound to Thermus thermophilus RNA polymerase beta-flap domain

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

DNA-directed RNA polymerase subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

Putative uncharacterized protein

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

3wof__assembly_2__model_1

3wof__assembly_2__model_1 | I(q)

3wof__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

7. Citations (1)

Crystal structure of P23-45 gp39 (6-132) bound to Thermus thermophilus RNA polymerase beta-flap domain

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

DNA-directed RNA polymerase subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Putative uncharacterized protein

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

3wof__assembly_2__model_1

3wof__assembly_2__model_1 | I(q)

3wof__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

7. Citations (1)