SAXSdb — 1d5a

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

PROTEIN (DNA POLYMERASE)

Desulfurococcus sp. Tok

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–733	Not recorded	SO4 SULFATE ION × 9 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.40 Å R-free 0.299

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q7SIG8_9CREN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–733； UniProt 1–733

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	1d5a
Deposition date deposition_date	1999-10-06
Structure title title	CRYSTAL STRUCTURE OF AN ARCHAEBACTERIAL DNA POLYMERASE D.TOK. DEPOSITION OF SECOND NATIVE STRUCTURE AT 2.4 ANGSTROM
Keywords keywords	DNA POLYMERASE, THERMOSTABLE, EXONUCLEASE, RBD DOMAIN, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	31.44 Å
Radius of gyration Rg (electron density) rg_electron	30.45 Å
Forward intensity I(0) i0	115388000.00
Molecular weight molecular_weight	85666.0 kDa
Excluded volume excluded_volume	107590 Å³
Envelope volume envelope_volume	144800 Å³
Hydration-shell volume shell_volume	39416 Å³
Envelope diameter envelope_diameter	98.8 Å
Shell Rg shell_rg	37.90 Å
Envelope Rg envelope_rg	29.82 Å
Shape Rg shape_rg	30.44 Å
Total Rg total_rg	31.17 Å
Total atoms total_atoms	6039
Residues n_residues	733
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	97.5 Å
Rg (real space) rg_real	31.28 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	1.1540e+08
I(0) uncertainty (real space) i0_real_error	1.8130e+06
Rg (reciprocal space) rg_reciprocal	31.35 Å
I(0) (reciprocal space) i0_reciprocal	115400000.0000
Solution quality estimate total_estimate	0.9086
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	41.0 Å
Skewness Skewness skewness	0.115
Kurtosis Kurtosis kurtosis	-0.602
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	25940000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.954; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.949

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	PROTEIN (DNA POLYMERASE)
Molecular weight formula_weight	84906.0 kDa
EC 编号 ec_number	2.7.7.7
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	6144

MILDADYITEDGKPVIRVFKKEKGEFKIDYDRDFEPYIYALLKDDSAIEDIKKITAERHGTTVRVTRAERVKKKFLGRPVEVWKLYFTHPQDVPAIRDKIREHPAVVDIYEYDIPFAKRYLIDRGLIPMEGDEELRMLAFDIETLAHAGAAAGAGPILMISYADEEGARVITWKNIDLPYVESVSTEKEMIKRFLKVIQEKDPDVLITYNGDNFDFAYLKKRSEMLGVKFILGRDGSEPKIQRMGDRFAVEVKGRIHFDLYPVIRRTINLPTYTLETVYEPVFGQPAEKVYAEEIAEAWASGEGLERVARYSMEDAKATYELGKEFFPMEAQLSRLVGQSLWDVSRSSTGNLVEWFLLRKAYERNDVAPNKPDERELARRTESYAGGYVKEPEKGLWENIVYLDYKSLYPSIIITHNVSPDTLNREGCREYDVAPQVGHRFCKDFPGFIPSLLGDLLEERQKVKKKMKATVDPIERKLLDYRQRAIKILANSYYGYYAYANARWYCRECAESVTAWGRQYIETTMREIEEKFGFKVLYADTDGFFATIPGADAETVKNKAKEFLNYINPRLPGLLELEYEGFYRRGFFVTKKKYAVIDEEDKITTRGLEIVRRDWSEIAKETQARVLEAILKHGDVEEAVRIVKEVTEKLSRHEVPPEKLVIYEAGPHVAAAATVISYIVLKGPGRVGDRAIPFDEFDPAKHRYDAEYYIENQVLPAVERILRAFGYRKEDLR

来源 Source

来源生物 organism	Desulfurococcus sp. Tok
NCBI Class编号 ncbi_taxonomy_id	108142
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 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	105

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1d5aa1
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	d1d5aa2
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 (4 domains)

Domain ID domain_id	1d5aA01
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	1d5aA02
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	1d5aA03
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	1d5aA04
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

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8. Citations (1)

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Unit-cell length a length_a	64.800 Å
Unit-cell length b length_b	107.600 Å
Unit-cell length c length_c	153.200 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	2.400 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2525
R_work r_work	0.2525
R_free r_free	0.2989

fit	/app/data/saxs_computation/d5/1d5a/1d5a.fit
pddf	/app/data/pr_computation/d5/1d5a/1d5a.pr.out
profile	/app/data/saxs_computation/d5/1d5a/1d5a.dat

CRYSTAL STRUCTURE OF AN ARCHAEBACTERIAL DNA POLYMERASE D.TOK. DEPOSITION OF SECOND NATIVE STRUCTURE AT 2.4 ANGSTROM

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

PROTEIN (DNA POLYMERASE)

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction