SAXSdb — 1cs3

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

ZINC FINGER PROTEIN PLZF

Homo sapiens

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 7–122	Fragment：BTB/POZ	MG MAGNESIUM ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；VAPOR DIFFUSION BY 8% ISOPROPANOL, 600mM MAGNESIUM CHLORIDE, 50mM HEPES 7.5 and 50mM TRIS 8.5, pH 8.00	Resolution 2.00 Å R-free 0.272
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 7–122	Fragment：BTB/POZ	MG MAGNESIUM ION × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；VAPOR DIFFUSION BY 8% ISOPROPANOL, 600mM MAGNESIUM CHLORIDE, 50mM HEPES 7.5 and 50mM TRIS 8.5, pH 8.00	Resolution 2.00 Å R-free 0.272

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 1CS3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BUO BTB DOMAIN FROM PLZF Deposited 1998-09-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 6–126（121 aa） Fragment：BTB DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.15 M CACL2, 0.1 M HEPES (PH 7.5), 4% ISOPROPANOL,	Resolution 1.90 Å R-free 0.252
8YTH Crystal structures of human IRF2BP2 RING domain in complex with ZBTB16 peptide Deposited 2024-03-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 285–292（8 aa）	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M potassium thiocyanate and 30% (w/v) PEG MME 2000	Resolution 2.40 Å R-free 0.281

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

View Construct and Data Evidence

UniProt name	ZBT16_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–116； UniProt 7–122

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	1cs3
Deposition date deposition_date	1999-08-16
Structure title title	STRUCTURE OF BTB/POZ TRANSCRIPTION REPRESSION DOMAIN FROM PROMELOCYTIC LEUKEMIA ZINC FINGER ONCOPROTEIN
Keywords keywords	BTB/POZ, PLZF, TRANSCRIPTION REPRESSION, ONCOPROTEIN, GENE REGULATION, TRANSCRIPTION; TRANSCRIPTION
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	16.71 Å
Radius of gyration Rg (electron density) rg_electron	15.68 Å
Forward intensity I(0) i0	3609380.00
Molecular weight molecular_weight	13421.0 kDa
Excluded volume excluded_volume	16841 Å³
Envelope volume envelope_volume	20675 Å³
Hydration-shell volume shell_volume	11892 Å³
Envelope diameter envelope_diameter	67.2 Å
Shell Rg shell_rg	20.70 Å
Envelope Rg envelope_rg	16.84 Å
Shape Rg shape_rg	15.59 Å
Total Rg total_rg	16.98 Å
Total atoms total_atoms	938
Residues n_residues	116
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	66.4 Å
Rg (real space) rg_real	16.79 Å
Rg uncertainty (real space) rg_real_error	0.59 Å
I(0) (real space) i0_real	3.6090e+06
I(0) uncertainty (real space) i0_real_error	4.7320e+04
Rg (reciprocal space) rg_reciprocal	16.78 Å
I(0) (reciprocal space) i0_reciprocal	3609000.0000
Solution quality estimate total_estimate	0.6297
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.8 Å
Skewness Skewness skewness	0.604
Kurtosis Kurtosis kurtosis	0.621
Angular range angular_range	— – 0.4750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	460300.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.416; Stabil: 1.000; Sysdev: 0.394; Positv: 1.000; Valcen: 0.769; Smooth: 0.983

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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	ZINC FINGER PROTEIN PLZF
Molecular weight formula_weight	13324.3 kDa
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	999

GMIQLQNPSHPTGLLCKANQMRLAGTLCDVVIMVDSQEFHAHRTVLACTSKMFEILFHRNSQHYTLDFLSPKTFQQILEYAYTATLQAKAEDLDDLLYAAEILEIEYLEEQCLKML

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	61

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1cs3a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.42 — POZ domain
Superfamily Superfamily superfamily	d.42.1 — POZ domain
Family Family family	d.42.1.1 — BTB/POZ domain

CATH v4.4 (1 domains)

Domain ID domain_id	1cs3A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily	10 — Potassium Channel Kv1.1; Chain A

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8. Citations (1)

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Unit-cell length a length_a	38.800 Å
Unit-cell length b length_b	78.200 Å
Unit-cell length c length_c	85.200 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	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2280
R_work r_work	0.2280
R_free r_free	0.2720

fit	/app/data/saxs_computation/cs/1cs3/1cs3.fit
pddf	/app/data/pr_computation/cs/1cs3/1cs3.pr.out
profile	/app/data/saxs_computation/cs/1cs3/1cs3.dat

STRUCTURE OF BTB/POZ TRANSCRIPTION REPRESSION DOMAIN FROM PROMELOCYTIC LEUKEMIA ZINC FINGER ONCOPROTEIN

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

ZINC FINGER PROTEIN PLZF

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