SAXSdb — 3jxd

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

Repressor protein C2

Enterobacteria phage P22

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 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain L； UniProt 2–68 Chain R； UniProt 2–68	Fragment：N-terminal domain: UNP residues 2-68	5'-D(CPAPTPTPTPAPAPGPAPCPGPTPCPTPTPAPAPAPTPG)-3' × 2 RB RUBIDIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；277 K；Rubidium chloride, PEG 400, Tris-HCl, MgCl2, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.10 Å R-free 0.225

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 3JXD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ADR DETERMINATION OF THE NUCLEAR MAGNETIC RESONANCE STRUCTURE OF THE DNA-BINDING DOMAIN OF THE P22 C2 REPRESSOR (1-76) IN SOLUTION AND COMPARISON WITH THE DNA-BINDING DOMAIN OF THE 434 REPRESSOR Deposited 1993-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–76（76 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
2R1J Crystal Structure of the P22 c2 Repressor protein in complex with the synthetic operator 9T Deposited 2007-08-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain L 1–68（68 aa） Chain R 1–68（68 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；277 K；The initial crystallization solution contained 0.42 mM P22R NTD, 0.42 mM duplex d(5 TATTTAAGATATCTTAAATG3 ) -d(5 CATTTAAGATATCTTAAATA3 ), 45 mM Tris.HCl (pH 7.8), 19 mM NaCl, 1.9 mM glycerol, 11% PEG 400, 4.5 mM LiCl, 2.3mM MgCl2 and 0.91% MPD in a volume of 5.3 ul. The crystallization solution was equilibrated against a reservoir of 100 mM Tris.HCl (pH 7.8), 25% PEG 400, 10 mM LiCl, 5 mM MgCl2 and 2% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.53 Å R-free 0.225
3JXB Crystal structure of the P22 c2 repressor protein in complex with synthetic operator 9C Deposited 2009-09-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain C 2–68（67 aa） Fragment：N-terminal domain: UNP residues 2-68 Chain D 2–68（67 aa） Fragment：N-terminal domain: UNP residues 2-68	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；277 K；PEG 400, NaCl, Tris-HCl, MgCl2, LiCl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.67 Å R-free 0.226
3JXC Crystal structure of the P22 c2 repressor protein in complex with synthetic operator 9T in the presence of Tl+ Deposited 2009-09-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain L 2–68（67 aa） Fragment：N-terminal domain: UNP residues 2-68 Chain R 2–68（67 aa） Fragment：N-terminal domain: UNP residues 2-68	Not recorded	TL THALLIUM (I) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；277 K；PEG 400, Thallium acetate, Tris-HCl, Magnesium acetate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.208

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPC2_BPP22
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain L； PDBConstruct 1–67； UniProt 2–68 Author chain R； PDBConstruct 1–67； UniProt 2–68

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	3jxd
Deposition date deposition_date	2009-09-18
Structure title title	Crystal structure of the P22 c2 repressor protein in complex with synthetic operator 9C in the presence of Rb+
Keywords keywords	protein-DNA complex, DNA-binding, Repressor, Transcription, Transcription regulation, TRANSCRIPTION REGULATOR; TRANSCRIPTION REGULATOR
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	20.35 Å
Radius of gyration Rg (electron density) rg_electron	19.62 Å
Forward intensity I(0) i0	21118400.00
Molecular weight molecular_weight	27185.0 kDa
Excluded volume excluded_volume	30628 Å³
Envelope volume envelope_volume	37640 Å³
Hydration-shell volume shell_volume	16760 Å³
Envelope diameter envelope_diameter	68.0 Å
Shell Rg shell_rg	24.82 Å
Envelope Rg envelope_rg	19.76 Å
Shape Rg shape_rg	19.47 Å
Total Rg total_rg	20.54 Å
Total atoms total_atoms	1846
Residues n_residues	172
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	63.1 Å
Rg (real space) rg_real	20.38 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	2.1120e+07
I(0) uncertainty (real space) i0_real_error	2.6920e+05
Rg (reciprocal space) rg_reciprocal	20.37 Å
I(0) (reciprocal space) i0_reciprocal	21120000.0000
Solution quality estimate total_estimate	0.9065
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.8 Å
Skewness Skewness skewness	0.362
Kurtosis Kurtosis kurtosis	-0.407
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3649000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.958

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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	5'-D(CPAPTPTPTPAPAPGPAPCPGPTPCPTPTPAPAPAPTPG)-3'
Molecular weight formula_weight	6132.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	A,B
Atom count atom_count	2134

CATTTAAGACGTCTTAAATG

Entity 2 Entity 2 polymer

Description description	Repressor protein C2
Molecular weight formula_weight	7494.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,R

NTQLMGERIRARRKKLKIRQAALGKMVGVSNVAISQWERSETEPNGENLLALSKALQCSPDYLLKGD

来源 Source

来源生物 organism	Enterobacteria phage P22
通用名 common_name	Bacteriophage P22
NCBI Class编号 ncbi_taxonomy_id	10754
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	RUBIDIUM ION
Molecular weight formula_weight	85.5 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	288

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3jxdl_
Class class	a — All alpha proteins
Fold Fold fold	a.35 — lambda repressor-like DNA-binding domains
Superfamily Superfamily superfamily	a.35.1 — lambda repressor-like DNA-binding domains
Family Family family	a.35.1.2 — Phage repressors

Domain ID domain_id	d3jxdr_
Class class	a — All alpha proteins
Fold Fold fold	a.35 — lambda repressor-like DNA-binding domains
Superfamily Superfamily superfamily	a.35.1 — lambda repressor-like DNA-binding domains
Family Family family	a.35.1.2 — Phage repressors

CATH v4.4 (2 domains)

Domain ID domain_id	3jxdL00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

Domain ID domain_id	3jxdR00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

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8. Citations (1)

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Unit-cell length a length_a	64.007 Å
Unit-cell length b length_b	64.007 Å
Unit-cell length c length_c	101.623 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 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	41.340 Å
R factor r_factor	0.1830
R_work r_work	0.1800
R_free r_free	0.2250

fit	/app/data/saxs_computation/jx/3jxd/3jxd.fit
pddf	/app/data/pr_computation/jx/3jxd/3jxd.pr.out
profile	/app/data/saxs_computation/jx/3jxd/3jxd.dat

Crystal structure of the P22 c2 repressor protein in complex with synthetic operator 9C in the presence of Rb+

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

Repressor protein C2

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 (4)

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 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)