1xhz

Phi29 DNA polymerase, orthorhombic crystal form, ssDNA complex

Method: X-RAY DIFFRACTION

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

DNA polymerase

Bacillus phage phi29

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 1	5'-D(TPTPTPTP*T)-3' × 1 water × 1	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 1	5'-D(TPTPTPTP*T)-3' × 1 water × 1	Consistent with all polymers
3	Protein–DNA	Monomer	Protein 1 DNA 1	5'-D(TPTPTPTP*T)-3' × 1 water × 2	Consistent with all polymers
4	Protein–DNA	Monomer	Protein 1 DNA 1	5'-D(TPTPTPTP*T)-3' × 1 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPOL_BPPH2
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–575； UniProt 1–575 Author chain B； PDBConstruct 1–575； UniProt 1–575 Author chain C； PDBConstruct 1–575； UniProt 1–575 Author chain D； PDBConstruct 1–575； UniProt 1–575

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	1xhz
Deposition date deposition_date	2004-09-21
Structure title title	Phi29 DNA polymerase, orthorhombic crystal form, ssDNA complex
Keywords keywords	DNA polymerase, protein-primed, strand displacement, processivity, replication, TRANSFERASE-DNA COMPLEX; TRANSFERASE/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.

1xhz__assembly_1__model_1

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

Download this curve (.dat)

1xhz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1xhz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.16 Å
Rg (electron density)	26.15 Å
Total Rg	27.01 Å
Atom count	4765
Residues	575
Excluded volume	85736 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1xhz__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1xhz__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1xhz__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1xhz__assembly_4__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 (3)

Entity 1 Entity 1 polymer

Description description	5'-D(TPTPTPTP*T)-3'
Molecular weight formula_weight	1476.0 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,F,G,H
Atom count atom_count	19512

TTTTT

Entity 2 Entity 2 polymer

Description description	DNA polymerase
Molecular weight formula_weight	66720.9 kDa
EC 编号 ec_number	2.7.7.7
Mutation mutation	D12A D66A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

MKHMPRKMYSCAFETTTKVEDCRVWAYGYMNIEDHSEYKIGNSLDEFMAWVLKVQADLYFHNLKFAGAFIINWLERNGFKWSADGLPNTYNTIISRMGQWYMIDICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLKGDIDYHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFKQGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLDKEVRYAYRGGFTWLNDRFKEKEIGEGMVFDVNSLYPAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEFELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSNVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDKWTYIKTTSEGAIKQLAKLMLNSLYGKFASNPDVTGKVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWARYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDPKKLGYWAHESTFKRAKYLRQKTYIQDIYMKEVDGKLVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKVGFSRKMKPKPVQVPGGVVLVDDTFTIK

Source Source

Source organism organism	Bacillus phage phi29
NCBI taxonomy ID ncbi_taxonomy_id	10756
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	512

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6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1xhza1
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	d1xhza2
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	d1xhzb1
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	d1xhzb2
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	d1xhzc1
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	d1xhzc2
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	d1xhzd1
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	d1xhzd2
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

CATH v4.4 (24 domains)

Domain ID domain_id	1xhzA01
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	1xhzA02
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	1xhzA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1770 — TPR 1 domain of DNA polymerase
Homologous superfamily homologous superfamily	10 — TPR 1 domain of DNA polymerase

Domain ID domain_id	1xhzA04
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	1xhzA05
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily	20 — DNA polymerase; domain 5

Domain ID domain_id	1xhzA06
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily	30 — DNA polymerase; domain 6

Domain ID domain_id	1xhzB01
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	1xhzB02
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	1xhzB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1770 — TPR 1 domain of DNA polymerase
Homologous superfamily homologous superfamily	10 — TPR 1 domain of DNA polymerase

Domain ID domain_id	1xhzB04
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	1xhzB05
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily	20 — DNA polymerase; domain 5

Domain ID domain_id	1xhzB06
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily	30 — DNA polymerase; domain 6

Domain ID domain_id	1xhzC01
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	1xhzC02
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	1xhzC03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1770 — TPR 1 domain of DNA polymerase
Homologous superfamily homologous superfamily	10 — TPR 1 domain of DNA polymerase

Domain ID domain_id	1xhzC04
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	1xhzC05
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily	20 — DNA polymerase; domain 5

Domain ID domain_id	1xhzC06
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily	30 — DNA polymerase; domain 6

Domain ID domain_id	1xhzD01
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	1xhzD02
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	1xhzD03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1770 — TPR 1 domain of DNA polymerase
Homologous superfamily homologous superfamily	10 — TPR 1 domain of DNA polymerase

Domain ID domain_id	1xhzD04
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	1xhzD05
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily	20 — DNA polymerase; domain 5

Domain ID domain_id	1xhzD06
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily	30 — DNA polymerase; domain 6

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Unit-cell length a length_a	96.662 Å
Unit-cell length b length_b	150.397 Å
Unit-cell length c length_c	198.325 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	16

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

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	19.990 Å
R factor r_factor	0.2190
R_work r_work	0.2190
R_free r_free	0.2680

Phi29 DNA polymerase, orthorhombic crystal form, ssDNA complex

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

1xhz__assembly_1__model_1

1xhz__assembly_1__model_1 | I(q)

1xhz__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (8 domains)

CATH v4.4 (24 domains)

7. Citations (2)

Phi29 DNA polymerase, orthorhombic crystal form, ssDNA complex

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

1xhz__assembly_1__model_1

1xhz__assembly_1__model_1 | I(q)

1xhz__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (8 domains)

CATH v4.4 (24 domains)

7. Citations (2)