SAXSdb — 1czd

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

DNA POLYMERASE ACCESSORY PROTEIN G45

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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–228 Chain B； UniProt 1–228 Chain C； UniProt 1–228	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.6；277 K；60 mM PIPES 200 mM CASO4 0.1 % 1,4 Dioxane 15% Glycerol 15% PEG MME 5000, pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.45 Å R-free 0.259

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 1CZD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3U5Z Structure of T4 Bacteriophage clamp loader bound to the T4 clamp, primer-template DNA, and ATP analog Deposited 2011-10-11	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain F 1–228（228 aa） Chain G 1–228（228 aa） Chain H 1–228（228 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；9% PEG4k, 0.1M MES pH 6.5, 50mM NaCl, 25mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 3.50 Å R-free 0.279
3U5Z Structure of T4 Bacteriophage clamp loader bound to the T4 clamp, primer-template DNA, and ATP analog Deposited 2011-10-11	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain P 1–228（228 aa） Chain Q 1–228（228 aa） Chain R 1–228（228 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；9% PEG4k, 0.1M MES pH 6.5, 50mM NaCl, 25mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 3.50 Å R-free 0.279
3U60 Structure of T4 Bacteriophage Clamp Loader Bound To Open Clamp, DNA and ATP Analog Deposited 2011-10-11	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain F 1–228（228 aa） Chain G 1–228（228 aa） Chain H 1–228（228 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；295 K；20% PEG4k, 0.1M Tris pH7.5, 10mM MgCl2, 20mM NaCl, VAPOR DIFFUSION, temperature 295K	Resolution 3.34 Å R-free 0.282
3U61 Structure of T4 Bacteriophage Clamp Loader Bound To Closed Clamp, DNA and ATP Analog and ADP Deposited 2011-10-11	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain F 1–228（228 aa） Chain G 1–228（228 aa） Chain H 1–228（228 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 3 08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；10% PEG4k, 0.1M MES pH 6.5, 20mM NaCl, 10mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.20 Å R-free 0.305
6DRT Crystal structure of the processivity clamp GP45 complexed with recognition peptide of ligase from bacteriophage T4 Deposited 2018-06-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–228（228 aa） Chain B 1–228（228 aa） Chain C 1–228（228 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；PEG3350	Resolution 2.12 Å R-free 0.240
7D7D CryoEM structure of gp45-dependent transcription activation complex Deposited 2020-10-03	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain G 1–228（228 aa） Chain H 1–228（228 aa） Chain I 1–228（228 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å
8UH7 Structure of T4 Bacteriophage clamp loader bound to the T4 clamp, primer-template DNA, and ATP analog Deposited 2023-10-07	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain F 1–228（228 aa） Chain G 1–228（228 aa） Chain H 1–228（228 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 3 MG MAGNESIUM ION × 4 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；295 K；20% PEG4k, 0.1M Tris pH7.5, 10mM MgCl2, 20mM NaCl	Resolution 2.63 Å R-free 0.244
8UK9 Structure of T4 Bacteriophage clamp loader mutant D110C bound to the T4 clamp, primer-template DNA, and ATP analog Deposited 2023-10-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain F 1–228（228 aa） Chain G 1–228（228 aa） Chain H 1–228（228 aa）	Not recorded	AF3 ALUMINUM FLUORIDE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；298 K；0.1M MES pH 6.5, 9% PEG MME 5000, 6% 1-Propanol	Resolution 3.10 Å R-free 0.265
8UK9 Structure of T4 Bacteriophage clamp loader mutant D110C bound to the T4 clamp, primer-template DNA, and ATP analog Deposited 2023-10-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain R 1–228（228 aa） Chain S 1–228（228 aa） Chain T 1–228（228 aa）	Not recorded	AF3 ALUMINUM FLUORIDE × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 4 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6.5；298 K；0.1M MES pH 6.5, 9% PEG MME 5000, 6% 1-Propanol	Resolution 3.10 Å R-free 0.265
8UNF Cryo-EM structure of T4 Bacteriophage Clamp Loader with Sliding Clamp and DNA Deposited 2023-10-18	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric	Chain F 1–228（228 aa） Chain G 1–228（228 aa） Chain H 1–228（228 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 4 08T [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.15 Å
8UNH Cryo-EM structure of T4 Bacteriophage Clamp Loader with Sliding Clamp Deposited 2023-10-19	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain F 1–228（228 aa） Chain G 1–228（228 aa） Chain H 1–228（228 aa）	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.21 Å
9E5Y T4 Bacteriophage Replicative Polymerase Captured in Polymerase Exchange State 1 Deposited 2024-10-28	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain B 1–228（228 aa） Chain D 1–228（228 aa） Chain E 1–228（228 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
9EA2 T4 Bacteriophage Replicative Polymerase Captured in Polymerase Exchange State 2 Deposited 2024-11-10	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric	Chain B 1–228（228 aa） Chain D 1–228（228 aa） Chain E 1–228（228 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9EA3 T4 bacteriophage replicative holoenzyme containing triple mutations D75R, Q430E, and K432E in the exonuclease-deficient polymerase Deposited 2024-11-10	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain B 1–228（228 aa） Chain D 1–228（228 aa） Chain E 1–228（228 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.99 Å
9EA6 T4 Bacteriophage Replicative Polymerase Captured in Polymerase Exchange State 3 Deposited 2024-11-10	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 B 1–228（228 aa） Chain D 1–228（228 aa） Chain E 1–228（228 aa）	Not recorded	CA CALCIUM ION × 1 D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.74 Å

13 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DPA5_BPT4
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–228； UniProt 1–228 Author chain B； PDBConstruct 1–228； UniProt 1–228 Author chain C； PDBConstruct 1–228； UniProt 1–228

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	1czd
Deposition date deposition_date	1999-09-02
Structure title title	CRYSTAL STRUCTURE OF THE PROCESSIVITY CLAMP GP45 FROM BACTERIOPHAGE T4
Keywords keywords	BACTERIOPHAGE T4, PROCESSIVITY CLAMP, DNA REPLICATION, RING-SHAPED PROTEIN, GENE REGULATION; GENE REGULATION
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	34.09 Å
Radius of gyration Rg (electron density) rg_electron	33.16 Å
Forward intensity I(0) i0	84808800.00
Molecular weight molecular_weight	74554.0 kDa
Excluded volume excluded_volume	94005 Å³
Envelope volume envelope_volume	134350 Å³
Hydration-shell volume shell_volume	33244 Å³
Envelope diameter envelope_diameter	99.9 Å
Shell Rg shell_rg	41.07 Å
Envelope Rg envelope_rg	31.55 Å
Shape Rg shape_rg	33.19 Å
Total Rg total_rg	33.77 Å
Total atoms total_atoms	5250
Residues n_residues	684
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	97.2 Å
Rg (real space) rg_real	33.95 Å
Rg uncertainty (real space) rg_real_error	0.58 Å
I(0) (real space) i0_real	8.4810e+07
I(0) uncertainty (real space) i0_real_error	1.2450e+06
Rg (reciprocal space) rg_reciprocal	34.04 Å
I(0) (reciprocal space) i0_reciprocal	84820000.0000
Solution quality estimate total_estimate	0.8610
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	52.8 Å
Skewness Skewness skewness	-0.032
Kurtosis Kurtosis kurtosis	-0.876
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	48320000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.942; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.387

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1czda1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.2 — DNA polymerase processivity factor

Domain ID domain_id	d1czda2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.2 — DNA polymerase processivity factor

Domain ID domain_id	d1czdb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.2 — DNA polymerase processivity factor

Domain ID domain_id	d1czdb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.2 — DNA polymerase processivity factor

Domain ID domain_id	d1czdc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.2 — DNA polymerase processivity factor

Domain ID domain_id	d1czdc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.131 — DNA clamp
Superfamily Superfamily superfamily	d.131.1 — DNA clamp
Family Family family	d.131.1.2 — DNA polymerase processivity factor

CATH v4.4 (3 domains)

Domain ID domain_id	1czdA00
Class class	3 — Alpha Beta
Architecture architecture	70 — Box
Topology topology	10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1czdB00
Class class	3 — Alpha Beta
Architecture architecture	70 — Box
Topology topology	10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1czdC00
Class class	3 — Alpha Beta
Architecture architecture	70 — Box
Topology topology	10 — Proliferating Cell Nuclear Antigen
Homologous superfamily homologous superfamily	10 —

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8. Citations (1)

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Unit-cell length a length_a	66.177 Å
Unit-cell length b length_b	93.938 Å
Unit-cell length c length_c	141.820 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	12

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

Resolution resolution	2.450 Å
Low-resolution limit resolution_low	100.000 Å
R factor r_factor	—
R_work r_work	0.2320
R_free r_free	0.2590

Description description	DNA POLYMERASE ACCESSORY PROTEIN G45
Molecular weight formula_weight	24881.2 kDa
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	5250

CRYSTAL STRUCTURE OF THE PROCESSIVITY CLAMP GP45 FROM BACTERIOPHAGE T4

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

DNA POLYMERASE ACCESSORY PROTEIN G45

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (6 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

fit	/app/data/saxs_computation/cz/1czd/1czd.fit
pddf	/app/data/pr_computation/cz/1czd/1czd.pr.out
profile	/app/data/saxs_computation/cz/1czd/1czd.dat