1z1a

S. cerevisiae Sir1 ORC-interaction domain

Method: X-RAY DIFFRACTION Dmax: 80.8 Å Quality: GOOD

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

Regulatory protein SIR1

Saccharomyces cerevisiae

UniProt P21691

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 473–611 Fragment:ORC-1 interacting domain of Sir1p Mutation:C593A Non-standard monomer:Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;298 K;sodium acetate, PEG 400, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.50 Å R-free 0.274
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 473–611 Fragment:ORC-1 interacting domain of Sir1p Mutation:C593A Non-standard monomer:Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;298 K;sodium acetate, PEG 400, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.50 Å R-free 0.274

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.

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

View Construct and Data Evidence
UniProt name SIR1_YEAST
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–142; UniProt 473–611 Author chain B; PDBConstruct 4–142; UniProt 473–611

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 1z1a

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1z1a
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1z1a
Deposition date deposition_date2005-03-03
Structure title titleS. cerevisiae Sir1 ORC-interaction domain
Keywords keywordsnovel fold, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.04
Radius of gyration Rg (electron density) rg_electron24.43
Forward intensity I(0) i012253000.00
Molecular weight molecular_weight27884.0 kDa
Excluded volume excluded_volume35425 ų
Envelope volume envelope_volume48007 ų
Hydration-shell volume shell_volume17120 ų
Envelope diameter envelope_diameter82.7
Shell Rg shell_rg30.08
Envelope Rg envelope_rg23.90
Shape Rg shape_rg24.37
Total Rg total_rg25.39
Total atoms total_atoms1944
Residues n_residues230
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 dmax80.8
Rg (real space) rg_real25.08
Rg uncertainty (real space) rg_real_error0.59
I(0) (real space) i0_real1.2250e+07
I(0) uncertainty (real space) i0_real_error1.6440e+05
Rg (reciprocal space) rg_reciprocal25.07
I(0) (reciprocal space) i0_reciprocal12250000.0000
Solution quality estimate total_estimate0.8827
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary21.8
Skewness Skewness skewness0.250
Kurtosis Kurtosis kurtosis-0.667
Angular range angular_range— – 0.3150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1558000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.822; Smooth: 0.956

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1z1aa1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.339 — ORC1-binding domain
Superfamily Superfamily superfamilyd.339.1 — ORC1-binding domain
Family Family familyd.339.1.1 — ORC1-binding domain
Domain ID domain_idd1z1ab_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.339 — ORC1-binding domain
Superfamily Superfamily superfamilyd.339.1 — ORC1-binding domain
Family Family familyd.339.1.1 — ORC1-binding domain

8. Citations (1)

9. Files and Curves (10)