SAXSdb — 1zs4

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

Regulatory protein CII

Enterobacteria phage lambda

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 × 4 DNA 2 PDB declaration: hexameric（6） Consistent with all polymer counts	Chain A； UniProt 4–82 Chain B； UniProt 4–82 Chain C； UniProt 4–82 Chain D； UniProt 4–82	Not recorded	DNA - 27mer × 1 DNA - 27mer × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 4.8；295 K；PEG 550 MME, SODIUM ACETATE, pH 4.8, VAPOR DIFFUSION, temperature 295K	Resolution 1.70 Å R-free 0.228

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 1ZS4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1XWR Crystal structure of the coliphage lambda transcription activator protein CII Deposited 2004-11-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–97（97 aa） Chain B 1–97（97 aa） Chain C 1–97（97 aa） Chain D 1–97（97 aa）	Not recorded	IPA ISOPROPYL ALCOHOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；298 K；PEG 3350, isopropanol, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.56 Å R-free 0.286
1ZPQ STRUCTURE OF BACTERIOPHAGE LAMBDA CII protein Deposited 2005-05-17	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–97（97 aa） Chain B 1–97（97 aa） Chain C 1–97（97 aa） Chain D 1–97（97 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å R-free 0.286
8IGR Cryo-EM structure of CII-dependent transcription activation complex Deposited 2023-02-21	Different construct 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 A 1–97（97 aa） Chain B 1–97（97 aa） Chain C 1–97（97 aa） Chain D 1–97（97 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å

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

View Construct and Data Evidence

UniProt name	RPC2_LAMBD
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 5–83； UniProt 4–82 Author chain B； PDBConstruct 5–83； UniProt 4–82 Author chain C； PDBConstruct 5–83； UniProt 4–82 Author chain D； PDBConstruct 5–83； UniProt 4–82

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	1zs4
Deposition date deposition_date	2005-05-23
Structure title title	Structure of bacteriophage lambda cII protein in complex with DNA
Keywords keywords	HELIX-TURN-HELIX, TRANSCRIPTION ACTIVATOR, transcription-DNA COMPLEX; transcription/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	28.20 Å
Radius of gyration Rg (electron density) rg_electron	26.85 Å
Forward intensity I(0) i0	63376200.00
Molecular weight molecular_weight	52005.0 kDa
Excluded volume excluded_volume	60803 Å³
Envelope volume envelope_volume	81667 Å³
Hydration-shell volume shell_volume	26115 Å³
Envelope diameter envelope_diameter	92.8 Å
Shell Rg shell_rg	32.99 Å
Envelope Rg envelope_rg	27.19 Å
Shape Rg shape_rg	26.77 Å
Total Rg total_rg	27.60 Å
Total atoms total_atoms	3582
Residues n_residues	370
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	91.0 Å
Rg (real space) rg_real	28.23 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	6.3380e+07
I(0) uncertainty (real space) i0_real_error	8.9800e+05
Rg (reciprocal space) rg_reciprocal	28.22 Å
I(0) (reciprocal space) i0_reciprocal	63380000.0000
Solution quality estimate total_estimate	0.9035
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.5 Å
Skewness Skewness skewness	0.282
Kurtosis Kurtosis kurtosis	-0.518
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3658000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.951; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.930

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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	DNA - 27mer
Molecular weight formula_weight	8264.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	U
Atom count atom_count	4012

TACCTCGTTGCGTTTGTTTGCACGAAT

Entity 2 Entity 2 polymer

Description description	DNA - 27mer
Molecular weight formula_weight	8318.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	T

TATTCGTGCAAACAAACGCAACGAGGT

Entity 3 Entity 3 polymer

Description description	Regulatory protein CII
Molecular weight formula_weight	9321.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

GSHMANKRNEALRIESALLNKIAMLGTEKTAEAVGVDKSQISRWKRDWIPKFSMLLAVLEWGVVDDDMARLARQVAAILTNKK

来源 Source

来源生物 organism	Enterobacteria phage lambda
NCBI Class编号 ncbi_taxonomy_id	10710
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	417

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1zs4a1
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.35.1.9 — Bacteriophage CII protein

Domain ID domain_id	d1zs4a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1zs4b2
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.35.1.9 — Bacteriophage CII protein

Domain ID domain_id	d1zs4b3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1zs4c_
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.35.1.9 — Bacteriophage CII protein

Domain ID domain_id	d1zs4d_
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.35.1.9 — Bacteriophage CII protein

CATH v4.4 (4 domains)

Domain ID domain_id	1zs4A00
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	1zs4B00
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	1zs4C00
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	1zs4D00
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	44.771 Å
Unit-cell length b length_b	97.132 Å
Unit-cell length c length_c	59.869 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.36 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.2090
R_free r_free	0.2280

fit	/app/data/saxs_computation/zs/1zs4/1zs4.fit
pddf	/app/data/pr_computation/zs/1zs4/1zs4.pr.out
profile	/app/data/saxs_computation/zs/1zs4/1zs4.dat

Structure of bacteriophage lambda cII protein in complex with DNA

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

Regulatory protein CII

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

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (6 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)