SAXSdb — 2w9m

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

POLYMERASE X

DEINOCOCCUS RADIODURANS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 4 MERCURY (II) ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 3 MERCURY (II) ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9RX48_DEIRA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–572； UniProt 1–572 Author chain B； PDBConstruct 1–572； UniProt 1–572

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	2w9m
Deposition date deposition_date	2009-01-27
Structure title title	Structure of family X DNA polymerase from Deinococcus radiodurans
Keywords keywords	SAXS, DNA REPAIR, DNA POLYMERASE, DNA REPLICATION; DNA REPLICATION
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.

2w9m__assembly_2__model_1

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

Download this curve (.dat)

2w9m__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2w9m__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	26.59 Å
Rg (electron density)	25.84 Å
Total Rg	26.54 Å
Atom count	4238
Residues	559
Excluded volume	74851 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2w9m__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2w9m__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 (4)

Entity 1 Entity 1 polymer

Description description	POLYMERASE X
Molecular weight formula_weight	62200.9 kDa
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	8426

MTLPPDAPSRHRLVHALERTADLLDILGGEDFKSRAYRSAARSLEELNEETPELLAREFTGIPKVGKGIAAELSDFARSGTFAPLEAAAGQLPPGLLDLLGVRGLGPKKIRSLWLAGIDSLERLREAAESGELAGLKGFGAKSAATILENVVFLFEARQRQSLRAGLAVAEELAGALTDLSPAPAGDVRRGLETVRAAELTVTGTPDDVLARLPELTVQGDGVLSGDYEGVPVEIACAPAEARGALDLLRSGEHFAGQVQAAAQARGFTLTAGGLSRGDEVLPTPTEAVVFHALDLPFRPAEYREPEHDDLWQTLPDPAELVTVGDLRGMIHTHSTWSDGGASIREMAEATLTLGHEFLGTADHSRAAYYANGLTIERLREQLKEIRELQRAGLPIVAGSEVDILDDGSLDFPDDVLGELDYVVVSVHSNFTLDAARQTERLIRAVSHPLVTVLGHATGRLLLRRPGYALDLDAVLGACEANGTVVEINANAARLDLDWREALRWRERLKFAINTDAHVPGGLRDARYGVMQARKAGLTPAHVVNSLGRAEFLDFVARQRAARGAPGPADRAHHHHHH

Source Source

Source organism organism	DEINOCOCCUS RADIODURANS
NCBI taxonomy ID ncbi_taxonomy_id	1299
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 non-polymer

Description description	MERCURY (II) ION
Molecular weight formula_weight	200.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	77

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6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id	2w9mA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	110 — DNA polymerase beta, N-terminal domain-like

Domain ID domain_id	2w9mA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

Domain ID domain_id	2w9mA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily	10 — Beta Polymerase, domain 2

Domain ID domain_id	2w9mA04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	210 — Beta Polymerase; domain 3
Homologous superfamily homologous superfamily	10 — DNA polymerase, thumb domain

Domain ID domain_id	2w9mA05
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

Domain ID domain_id	2w9mB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	110 — DNA polymerase beta, N-terminal domain-like

Domain ID domain_id	2w9mB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	20 — 5' to 3' exonuclease, C-terminal subdomain

Domain ID domain_id	2w9mB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily	10 — Beta Polymerase, domain 2

Domain ID domain_id	2w9mB04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	210 — Beta Polymerase; domain 3
Homologous superfamily homologous superfamily	10 — DNA polymerase, thumb domain

Domain ID domain_id	2w9mB05
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	140 — Metal-dependent hydrolases

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Unit-cell length a length_a	58.930 Å
Unit-cell length b length_b	138.250 Å
Unit-cell length c length_c	67.750 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.25 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.460 Å
Low-resolution limit resolution_low	45.320 Å
R factor r_factor	0.2060
R_work r_work	0.2030
R_free r_free	0.2490

Structure of family X DNA polymerase from Deinococcus radiodurans

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

POLYMERASE X

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

2w9m__assembly_2__model_1

2w9m__assembly_2__model_1 | I(q)

2w9m__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)

Structure of family X DNA polymerase from Deinococcus radiodurans

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

POLYMERASE X

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

2w9m__assembly_2__model_1

2w9m__assembly_2__model_1 | I(q)

2w9m__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)