3zop

Arg90Cit chorismate mutase of Bacillus subtilis at 1.6 A resolution

Method: X-RAY DIFFRACTION Dmax: 94.8 Å Quality: GOOD

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

CHORISMATE MUTASE AROH

BACILLUS SUBTILIS

UniProt P19080

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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 1–127 Chain B; UniProt 1–127 Chain C; UniProt 1–127 Mutation:YES Non-standard monomer:Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:pH 6;100 MM MMT BUFFER ---MALIC ACID, MES, TRIS, IN MOLAR RATIOS OF 1:2:2, RESPECTIVELY--- PH 6.0, 150 MM CALCIUM CHLORIDE, 25% W/V PEG 1000 Resolution 1.61 Å R-free 0.221
2 Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 1–127 Chain E; UniProt 1–127 Chain F; UniProt 1–127 Mutation:YES Non-standard monomer:Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:pH 6;100 MM MMT BUFFER ---MALIC ACID, MES, TRIS, IN MOLAR RATIOS OF 1:2:2, RESPECTIVELY--- PH 6.0, 150 MM CALCIUM CHLORIDE, 25% W/V PEG 1000 Resolution 1.61 Å R-free 0.221

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.

9 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AROH_BACSU
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–127; UniProt 1–127 Author chain B; PDBConstruct 1–127; UniProt 1–127 Author chain C; PDBConstruct 1–127; UniProt 1–127 Author chain D; PDBConstruct 1–127; UniProt 1–127 Author chain E; PDBConstruct 1–127; UniProt 1–127 Author chain F; PDBConstruct 1–127; UniProt 1–127

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 3zop

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3zop
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3zop
Deposition date deposition_date2013-02-22
Structure title titleArg90Cit chorismate mutase of Bacillus subtilis at 1.6 A resolution
Keywords keywordsPSEUDO-ALPHA BETA-BARREL, ISOMERASE; ISOMERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier29.64
Radius of gyration Rg (electron density) rg_electron28.89
Forward intensity I(0) i0101737000.00
Molecular weight molecular_weight80218.0 kDa
Excluded volume excluded_volume100940 ų
Envelope volume envelope_volume123220 ų
Hydration-shell volume shell_volume35542 ų
Envelope diameter envelope_diameter93.8
Shell Rg shell_rg36.31
Envelope Rg envelope_rg28.70
Shape Rg shape_rg28.91
Total Rg total_rg29.53
Total atoms total_atoms5592
Residues n_residues696
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 dmax94.8
Rg (real space) rg_real29.69
Rg uncertainty (real space) rg_real_error0.56
I(0) (real space) i0_real1.0170e+08
I(0) uncertainty (real space) i0_real_error1.3760e+06
Rg (reciprocal space) rg_reciprocal29.67
I(0) (reciprocal space) i0_reciprocal101700000.0000
Solution quality estimate total_estimate0.8834
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary30.4
Skewness Skewness skewness0.378
Kurtosis Kurtosis kurtosis-0.545
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha64380000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.869; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.892

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd3zopa_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamilyd.79.1 — YjgF-like
Family Family familyd.79.1.2 — Chorismate mutase
Domain ID domain_idd3zopb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamilyd.79.1 — YjgF-like
Family Family familyd.79.1.2 — Chorismate mutase
Domain ID domain_idd3zopc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamilyd.79.1 — YjgF-like
Family Family familyd.79.1.2 — Chorismate mutase
Domain ID domain_idd3zopd_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamilyd.79.1 — YjgF-like
Family Family familyd.79.1.2 — Chorismate mutase
Domain ID domain_idd3zope_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamilyd.79.1 — YjgF-like
Family Family familyd.79.1.2 — Chorismate mutase
Domain ID domain_idd3zopf_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.79 — Bacillus chorismate mutase-like
Superfamily Superfamily superfamilyd.79.1 — YjgF-like
Family Family familyd.79.1.2 — Chorismate mutase

CATH v4.4 (6 domains)

Domain ID domain_id3zopA00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily40 — RutC-like
Domain ID domain_id3zopB00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily40 — RutC-like
Domain ID domain_id3zopC00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily40 — RutC-like
Domain ID domain_id3zopD00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily40 — RutC-like
Domain ID domain_id3zopE00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily40 — RutC-like
Domain ID domain_id3zopF00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily40 — RutC-like

8. Citations (1)

9. Files and Curves (10)