1x1w

Water-mediate interaction at aprotein-protein interface

Method: X-RAY DIFFRACTION Dmax: 98.4 Å Quality: GOOD

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

Ribonuclease

Bacillus amyloliquefaciens

UniProt P00648

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 48–157 Not recorded Barstar × 1 (P11540) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;VAPOR DIFFUSION, HANGING DROP Resolution 2.10 Å R-free 0.265
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 48–157 Not recorded Barstar × 1 (P11540) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;VAPOR DIFFUSION, HANGING DROP Resolution 2.10 Å R-free 0.265
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 48–157 Not recorded Barstar × 1 (P11540) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;VAPOR DIFFUSION, HANGING DROP Resolution 2.10 Å R-free 0.265

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.

51 other PDB entries and 135 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RNBR_BACAM
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–110; UniProt 48–157 Author chain B; PDBConstruct 1–110; UniProt 48–157 Author chain C; PDBConstruct 1–110; UniProt 48–157

Barstar

Bacillus amyloliquefaciens

UniProt P11540

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 0–89 Mutation:C40A, C82A, E80A Ribonuclease × 1 (P00648) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;VAPOR DIFFUSION, HANGING DROP Resolution 2.10 Å R-free 0.265
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 0–89 Mutation:C40A, C82A, E80A Ribonuclease × 1 (P00648) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;VAPOR DIFFUSION, HANGING DROP Resolution 2.10 Å R-free 0.265
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain F; UniProt 0–89 Mutation:C40A, C82A, E80A Ribonuclease × 1 (P00648) X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;VAPOR DIFFUSION, HANGING DROP Resolution 2.10 Å R-free 0.265

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.

20 other PDB entries and 48 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BARS_BACAM
Isoform
PDB entities 2
Chains and sequence ranges Author chain D; PDBConstruct 1–90; UniProt 0–89 Author chain E; PDBConstruct 1–90; UniProt 0–89 Author chain F; PDBConstruct 1–90; UniProt 0–89

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 1x1w

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1x1w
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id1x1w
Deposition date deposition_date2005-04-14
Structure title titleWater-mediate interaction at aprotein-protein interface
Keywords keywordsRnase-inhibitor complex, Hydrolase/Hydrolase inhibitor, Hydrolase-Protein Binding COMPLEX; Hydrolase/Protein Binding
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.27
Radius of gyration Rg (electron density) rg_electron29.80
Forward intensity I(0) i071314100.00
Molecular weight molecular_weight67226.0 kDa
Excluded volume excluded_volume84417 ų
Envelope volume envelope_volume106180 ų
Hydration-shell volume shell_volume30716 ų
Envelope diameter envelope_diameter102.0
Shell Rg shell_rg35.48
Envelope Rg envelope_rg29.80
Shape Rg shape_rg29.74
Total Rg total_rg30.56
Total atoms total_atoms4761
Residues n_residues596
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 dmax98.4
Rg (real space) rg_real30.26
Rg uncertainty (real space) rg_real_error0.67
I(0) (real space) i0_real7.1310e+07
I(0) uncertainty (real space) i0_real_error1.2010e+06
Rg (reciprocal space) rg_reciprocal30.27
I(0) (reciprocal space) i0_reciprocal71310000.0000
Solution quality estimate total_estimate0.8965
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary37.8
Skewness Skewness skewness0.260
Kurtosis Kurtosis kurtosis-0.512
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15990000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.930; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.898

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1x1wa_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.1 — Microbial ribonucleases
Superfamily Superfamily superfamilyd.1.1 — Microbial ribonucleases
Family Family familyd.1.1.2 — Bacterial ribonucleases
Domain ID domain_idd1x1wb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.1 — Microbial ribonucleases
Superfamily Superfamily superfamilyd.1.1 — Microbial ribonucleases
Family Family familyd.1.1.2 — Bacterial ribonucleases
Domain ID domain_idd1x1wc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.1 — Microbial ribonucleases
Superfamily Superfamily superfamilyd.1.1 — Microbial ribonucleases
Family Family familyd.1.1.2 — Bacterial ribonucleases
Domain ID domain_idd1x1wd1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.9 — Barstar-like
Superfamily Superfamily superfamilyc.9.1 — Barstar-related
Family Family familyc.9.1.1 — Barstar-related
Domain ID domain_idd1x1we_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.9 — Barstar-like
Superfamily Superfamily superfamilyc.9.1 — Barstar-related
Family Family familyc.9.1.1 — Barstar-related
Domain ID domain_idd1x1wf_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.9 — Barstar-like
Superfamily Superfamily superfamilyc.9.1 — Barstar-related
Family Family familyc.9.1.1 — Barstar-related

CATH v4.4 (6 domains)

Domain ID domain_id1x1wA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily30 — Microbial ribonucleases
Domain ID domain_id1x1wB00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily30 — Microbial ribonucleases
Domain ID domain_id1x1wC00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily30 — Microbial ribonucleases
Domain ID domain_id1x1wD00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology370 — Barnase; Chain D
Homologous superfamily homologous superfamily10 — Barstar-like
Domain ID domain_id1x1wE00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology370 — Barnase; Chain D
Homologous superfamily homologous superfamily10 — Barstar-like
Domain ID domain_id1x1wF00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology370 — Barnase; Chain D
Homologous superfamily homologous superfamily10 — Barstar-like

8. Citations (1)

9. Files and Curves (10)