SAXSdb — 1noy

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

PROTEIN (DNA POLYMERASE (E.C.2.7.7.7))

Enterobacteria phage T4

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–DNA Homooligomer Protein × 2 DNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain A； UniProt 1–388 Chain B； UniProt 1–388	Not recorded	;DNA (5'-D(TPTP*T)-3') ; × 1 ZN ZINC ION × 1 MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.20 Å

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.

Other PDB	Difference from Current Entry 1NOY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1NOZ T4 DNA POLYMERASE FRAGMENT (RESIDUES 1-388) AT 110K Deposited 1996-02-16	Different construct Different oligomeric state Different ligand/ion	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–388（388 aa） Fragment：RESIDUES 1 - 388 Chain B 1–388（388 aa） Fragment：RESIDUES 1 - 388	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
1NOZ T4 DNA POLYMERASE FRAGMENT (RESIDUES 1-388) AT 110K Deposited 1996-02-16	Different construct Different oligomeric state Different ligand/ion	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–388（388 aa） Fragment：RESIDUES 1 - 388 Chain B 1–388（388 aa） Fragment：RESIDUES 1 - 388	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
9E5Y T4 Bacteriophage Replicative Polymerase Captured in Polymerase Exchange State 1 Deposited 2024-10-28	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain A 1–898（898 aa） Chain C 1–898（898 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.57 Å

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DPOL_BPT4
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–388； UniProt 1–388 Author chain B； PDBConstruct 1–388； UniProt 1–388

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	1noy
Deposition date deposition_date	1996-02-16
Structure title title	DNA POLYMERASE (E.C.2.7.7.7)/DNA COMPLEX
Keywords keywords	EXONUCLEASE, DNA-BINDING, COMPLEX (NUCLEOTIDYLTRANSFERASE-DNA), TRANSFERASE-DNA complex; TRANSFERASE/DNA
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	32.64 Å
Radius of gyration Rg (electron density) rg_electron	32.12 Å
Forward intensity I(0) i0	110500000.00
Molecular weight molecular_weight	84731.0 kDa
Excluded volume excluded_volume	106290 Å³
Envelope volume envelope_volume	133430 Å³
Hydration-shell volume shell_volume	36246 Å³
Envelope diameter envelope_diameter	112.6 Å
Shell Rg shell_rg	37.31 Å
Envelope Rg envelope_rg	31.87 Å
Shape Rg shape_rg	32.10 Å
Total Rg total_rg	32.62 Å
Total atoms total_atoms	5951
Residues n_residues	721
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	112.5 Å
Rg (real space) rg_real	32.88 Å
Rg uncertainty (real space) rg_real_error	1.12 Å
I(0) (real space) i0_real	1.1050e+08
I(0) uncertainty (real space) i0_real_error	1.8310e+06
Rg (reciprocal space) rg_reciprocal	32.78 Å
I(0) (reciprocal space) i0_reciprocal	110500000.0000
Solution quality estimate total_estimate	0.8556
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.1 Å
Skewness Skewness skewness	0.496
Kurtosis Kurtosis kurtosis	-0.325
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	24490000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.785; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.862; Smooth: 0.902

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(TPTP*T)-3') ;
Molecular weight formula_weight	867.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	S
Atom count atom_count	6130

TTT

Entity 2 Entity 2 polymer

Description description	PROTEIN (DNA POLYMERASE (E.C.2.7.7.7))
Molecular weight formula_weight	45315.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MDEFYISIETVGNNIVERYIDENGKERTREVEYLPTMFRHCKEESKYKDIYGKNCAPQKFPSMKDARDWMKRMEDIGLEALGMNDFKLAYISDTYGSEIVYDRKFVRVANCDIEVTGDKFPDPMKAEYEIDAITHYDSIDDRFYVFDLLNSMYGSVSKWDAKLAAKLDCEGGDEVPQEILDRVIYMPFDNERDMLMEYINLWEQKRPAIFTGWNIEGFDVPYIMNRVKMILGERSMKRFSPIGRVKSKLLQNMYGSKEIYSIDGVSILDYLDLYKKFAFTNLPSFSLESVAQHETKKGKLPYDGPINKLRETNHQRYISYNIIDVESVQAIDKIRGFIDLVLSMSYYAKMPFSGVMSPIKTWDAIIFNSLKGEHKVIPQQGSHVKQSF

来源 Source

来源生物 organism	Enterobacteria phage T4
NCBI Class编号 ncbi_taxonomy_id	10665
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	179

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1noya_
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	d1noyb_
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

CATH v4.4 (4 domains)

Domain ID domain_id	1noyA01
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	1noyA02
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	1noyB01
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	1noyB02
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

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8. Citations (3)

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Unit-cell length a length_a	114.701 Å
Unit-cell length b length_b	109.656 Å
Unit-cell length c length_c	70.268 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	—
R_work r_work	0.2220
R_free r_free	—

fit	/app/data/saxs_computation/no/1noy/1noy.fit
pddf	/app/data/pr_computation/no/1noy/1noy.pr.out
profile	/app/data/saxs_computation/no/1noy/1noy.dat

DNA POLYMERASE (E.C.2.7.7.7)/DNA COMPLEX

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

PROTEIN (DNA POLYMERASE (E.C.2.7.7.7))

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

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)