SAXSdb — 5a7u

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

REGULATORY PROTEIN ADR1

SACCHAROMYCES CEREVISIAE

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 130–158	Fragment：RESIDUES 130-158	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer：20 MM HEPES PH 7.2 , 50 MM KOAC, 5 MM MG OAC2, 0.03% DDM, 50 MICROM ZNCL2, 125 MM SUCROSE.；pH 7.2；20 MM HEPES PH 7.2 , 50 MM KOAC, 5 MM MG OAC2, 0.03% DDM, 50 MICROM ZNCL2, 125 MM SUCROSE. cryo-EM vitrification conditions：Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, INSTRUMENT- FEI VITROBOT MARK IV,	Resolution 4.80 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 5A7U	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ARD STRUCTURES OF DNA-BINDING MUTANT ZINC FINGER DOMAINS: IMPLICATIONS FOR DNA BINDING Deposited 1993-10-01	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 102–130（29 aa）	Not recorded	ZN ZINC ION × 1	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1ARE STRUCTURES OF DNA-BINDING MUTANT ZINC FINGER DOMAINS: IMPLICATIONS FOR DNA BINDING Deposited 1993-10-01	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 102–130（29 aa）	Not recorded	ZN ZINC ION × 1	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1ARF STRUCTURES OF DNA-BINDING MUTANT ZINC FINGER DOMAINS: IMPLICATIONS FOR DNA BINDING Deposited 1993-10-01	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 102–130（29 aa）	Not recorded	ZN ZINC ION × 1	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1PAA STRUCTURE OF A HISTIDINE-X4-HISTIDINE ZINC FINGER DOMAIN: INSIGHTS INTO ADR1-UAS1 PROTEIN-DNA RECOGNITION Deposited 1994-07-15	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 130–159（30 aa）	Not recorded	ZN ZINC ION × 1	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
2ADR ADR1 DNA-BINDING DOMAIN FROM SACCHAROMYCES CEREVISIAE, NMR, 25 STRUCTURES Deposited 1998-03-20	Different construct Different mutation/modification 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 102–161（60 aa） Fragment：DNA-BINDING DOMAIN	Mutation：C140A	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 5.5；303 K	Resolution not provided

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ADR1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–29； UniProt 130–158

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	5a7u
Deposition date deposition_date	2015-07-10
Structure title title	Single-particle cryo-EM of co-translational folded adr1 domain inside the E. coli ribosome exit tunnel.
Keywords keywords	PROTEIN FOLDING, TRANSLATION, RIBOSOME, ZINC FINGER, SECM, TRANSLATIONAL ARREST PEPTIDE, CRYO-EM, SINGLE- MOLECULE STUDIES; TRANSLATION
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	10.04 Å
Radius of gyration Rg (electron density) rg_electron	8.63 Å
Forward intensity I(0) i0	321355.00
Molecular weight molecular_weight	3247.0 kDa
Excluded volume excluded_volume	3997 Å³
Envelope volume envelope_volume	4428 Å³
Hydration-shell volume shell_volume	4817 Å³
Envelope diameter envelope_diameter	29.1 Å
Shell Rg shell_rg	13.14 Å
Envelope Rg envelope_rg	8.97 Å
Shape Rg shape_rg	8.62 Å
Total Rg total_rg	10.20 Å
Total atoms total_atoms	455
Residues n_residues	27
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	32.6 Å
Rg (real space) rg_real	10.01 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	3.2140e+05
I(0) uncertainty (real space) i0_real_error	3.0410e+03
Rg (reciprocal space) rg_reciprocal	10.01 Å
I(0) (reciprocal space) i0_reciprocal	321400.0000
Solution quality estimate total_estimate	0.7591
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	12.4 Å
Skewness Skewness skewness	0.184
Kurtosis Kurtosis kurtosis	-0.399
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	24240.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.929; Stabil: 1.000; Sysdev: 0.368; Positv: 1.000; Valcen: 0.989; Smooth: 0.985

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Resolution resolution	4.800 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	4.80 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	151900

Description description	REGULATORY PROTEIN ADR1
Molecular weight formula_weight	3406.0 kDa
Source method src_method	man
Copy count entity_count	1

Single-particle cryo-EM of co-translational folded adr1 domain inside the E. coli ribosome exit tunnel.

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

REGULATORY PROTEIN ADR1

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	455

来源生物 organism	SACCHAROMYCES CEREVISIAE
通用名 common_name	;BAKER'S YEAST ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	ESCHERICHIA COLI

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

fit	/app/data/saxs_computation/a7/5a7u/5a7u.fit
pddf	/app/data/pr_computation/a7/5a7u/5a7u.pr.out
profile	/app/data/saxs_computation/a7/5a7u/5a7u.dat