1atg

AZOTOBACTER VINELANDII PERIPLASMIC MOLYBDATE-BINDING PROTEIN

Method: X-RAY DIFFRACTION Dmax: 60.7 Å Quality: REASONABLE

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

PERIPLASMIC MOLYBDATE-BINDING PROTEIN

OrganismNot specified

UniProt Q7SIH2

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 1–231 Not recorded WO4 TUNGSTATE(VI)ION × 1 ACT ACETATE ION × 1 SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4;291 K;HANGING DROP VAPOUR DIFFUSION WITH PROTEIN CONCENTRATION IN THE RANGE 10-15 MG/ML IN 10MM TRIS-HCL PH 7.0. 1 OR 2 MICROLITER DROPS OF THE LATTER WERE MIXED WITH AN EQUAL VOLUME OF 11-14% (W/V) PEG 4000 AND 0.4M AMMONIUM SULFATE IN 0.1M ACETATE BUFFER AT PH 4.0, AND THEN EQUILIBRATED AGAINST THIS SOLUTION AT 18 DEG C. CRYOPROTECTED USING THE SAME SOLUTION CONTAINING 25% (V/V) ETHYLENE GLYCOL., vapor diffusion - hanging drop, temperature 291K Resolution 1.20 Å R-free 0.183

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name Q7SIH2_AZOVI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–231; UniProt 1–231

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1atg

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1atg
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1atg
Deposition date deposition_date1997-08-14
Structure title titleAZOTOBACTER VINELANDII PERIPLASMIC MOLYBDATE-BINDING PROTEIN
Keywords keywordsMOLYBDATE, TUNGSTATE, BINDING PROTEIN, PERIPLASM, ABC TRANSPORTER; BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier18.68
Radius of gyration Rg (electron density) rg_electron17.82
Forward intensity I(0) i010862200.00
Molecular weight molecular_weight24841.0 kDa
Excluded volume excluded_volume31176 ų
Envelope volume envelope_volume34710 ų
Hydration-shell volume shell_volume16572 ų
Envelope diameter envelope_diameter60.4
Shell Rg shell_rg23.51
Envelope Rg envelope_rg18.17
Shape Rg shape_rg17.85
Total Rg total_rg18.63
Total atoms total_atoms1743
Residues n_residues231
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax60.7
Rg (real space) rg_real18.68
Rg uncertainty (real space) rg_real_error0.36
I(0) (real space) i0_real1.0860e+07
I(0) uncertainty (real space) i0_real_error1.2860e+05
Rg (reciprocal space) rg_reciprocal18.68
I(0) (reciprocal space) i0_reciprocal10860000.0000
Solution quality estimate total_estimate0.7002
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.6
Skewness Skewness skewness0.367
Kurtosis Kurtosis kurtosis-0.307
Angular range angular_range— – 0.4250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2357000.0000
Real-space data points n_real_points74
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.843; Stabil: 1.000; Sysdev: 0.197; Positv: 1.000; Valcen: 0.996; Smooth: 0.985

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1atga_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamilyc.94.1 — Periplasmic binding protein-like II
Family Family familyc.94.1.1 — Phosphate binding protein-like

CATH v4.4 (2 domains)

Domain ID domain_id1atgA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II
Domain ID domain_id1atgA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily10 — Periplasmic binding protein-like II

8. Citations (2)

9. Files and Curves (10)