SAXSdb — 1q9y

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

DNA POLYMERASE

Enterobacteria phage RB69

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 2	5'-AC(8-OXOGUANOSINE)GGTAAGCAGTCCGCG-3' × 1 5'-GCGGACTGCTTAC(DIDEOXYCYTIDINE)-3' × 1 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 CALCIUM ION × 3 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPOL_BPR69
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 4–906； UniProt 1–903

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	1q9y
Deposition date deposition_date	2003-08-26
Structure title title	CRYSTAL STRUCTURE OF ENTEROBACTERIA PHAGE RB69 GP43 DNA POLYMERASE COMPLEXED WITH 8-OXOGUANOSINE CONTAINING DNA
Keywords keywords	PROTEIN_DNA COMPLEX, TRANSFERASE, REPLICATION-DNA COMPLEX; TRANSFERASE, REPLICATION/DNA
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.

1q9y__assembly_1__model_1

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

Download this curve (.dat)

1q9y__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1q9y__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.97 Å
Rg (electron density)	30.88 Å
Total Rg	31.59 Å
Atom count	8039
Residues	932
Excluded volume	141260 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1q9y__assembly_1__model_1`	trimeric （3）	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 (6)

Entity 1 Entity 1 polymer

Description description	5'-AC(8-OXOGUANOSINE)GGTAAGCAGTCCGCG-3'
Molecular weight formula_weight	5582.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	T
Atom count atom_count	8123

ACGGGTAAGCAGTCCGCG

Entity 2 Entity 2 polymer

Description description	5'-GCGGACTGCTTAC(DIDEOXYCYTIDINE)-3'
Molecular weight formula_weight	4240.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	P

GCGGACTGCTTACC

Entity 3 Entity 3 polymer

Description description	DNA POLYMERASE
Molecular weight formula_weight	104937.4 kDa
EC 编号 ec_number	2.7.7.7
Mutation mutation	D222A, D327A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

HGSMKEFYLTVEQIGDSIFERYIDSNGRERTREVEYKPSLFAHCPESQATKYFDIYGKPCTRKLFANMRDASQWIKRMEDIGLEALGMDDFKLAYLSDTYNYEIKYDHTKIRVANFDIEVTSPDGFPEPSQAKHPIDAITHYDSIDDRFYVFDLLNSPYGNVEEWSIEIAAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAKRLSPHRKTRVKVIENMYGSREIITLFGISVLDYIDLYKKFSFTNQPSYSLDYISEFELNVGKLKYDGPISKLRESNHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVFSPIKTWDAIIFNSLKEQNKVIPQGRSHPVQPYPGAFVKEPIPNRYKYVMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAERPSDVYSCSPNGMMYYKDRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNLSVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKLLINSLYGALGNVWFRYYDLRNATAITTFGQMALQWIERKVNEYLNEVCGTEGEAFVLYGDTDSIYVSADKIIDKVGESKFRDTNHWVDFLDKFARERMEPAIDRGFREMCEYMNNKQHLMFMDREAIAGPPLGSKGIGGFWTGKKRYALNVWDMEGTRYAEPKLKIMGLETQKSSTPKAVQKALKECIRRMLQEGEESLQEYFKEFEKEFRQLNYISIASVSSANNIAKYDVGGFPGPKCPFHIRGILTYNRAIKGNIDAPQVVEGEKVYVLPLREGNPFGDKCIAWPSGTEITDLIKDDVLHWMDYTVLLEKTFIKPLEGFTSAAKLDYEKKASLFDMFDF

Source Source

Source organism organism	Enterobacteria phage RB69
NCBI taxonomy ID ncbi_taxonomy_id	12353
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	467.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	84

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1q9ya1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.3 — Ribonuclease H-like
Family Family family	c.55.3.5 — DnaQ-like 3'-5' exonuclease

Domain ID domain_id	d1q9ya2
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.8 — DNA/RNA polymerases
Superfamily Superfamily superfamily	e.8.1 — DNA/RNA polymerases
Family Family family	e.8.1.1 — DNA polymerase I

Domain ID domain_id	d1q9ya3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id	1q9yA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	342 — DNA Polymerase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — DNA Polymerase, chain B, domain 1

Domain ID domain_id	1q9yA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

Domain ID domain_id	1q9yA03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1600 — Palm domain of DNA polymerase
Homologous superfamily homologous superfamily	10 — B family DNA polymerase, palm domain

Domain ID domain_id	1q9yA04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	690 — B family DNA polymerase, finger domain

Domain ID domain_id	1q9yA05
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1280 — Monooxygenase
Homologous superfamily homologous superfamily	300 —

Domain ID domain_id	1q9yA06
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1820 — Ribonuclease H-like motif
Homologous superfamily homologous superfamily	10 — DnaQ-like 3'-5' exonuclease

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Unit-cell length a length_a	80.822 Å
Unit-cell length b length_b	118.565 Å
Unit-cell length c length_c	127.224 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	4

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	46.060 Å
R factor r_factor	0.2073
R_work r_work	0.2039
R_free r_free	0.2707

CRYSTAL STRUCTURE OF ENTEROBACTERIA PHAGE RB69 GP43 DNA POLYMERASE COMPLEXED WITH 8-OXOGUANOSINE CONTAINING DNA

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

DNA POLYMERASE

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

1q9y__assembly_1__model_1

1q9y__assembly_1__model_1 | I(q)

1q9y__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

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 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF ENTEROBACTERIA PHAGE RB69 GP43 DNA POLYMERASE COMPLEXED WITH 8-OXOGUANOSINE CONTAINING DNA

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

DNA POLYMERASE

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

1q9y__assembly_1__model_1

1q9y__assembly_1__model_1 | I(q)

1q9y__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

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 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (1)