← Back to search
1cvr

Crystal structure of the Arg specific cysteine proteinase gingipain R (RGPB)

Method: X-RAY DIFFRACTION Dmax: 71.9 Å Quality: GOOD
▼

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

GINGIPAIN R

Porphyromonas gingivalis

UniProt P95493

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 230–664 Not recorded H37 D-phenylalanyl-N-[(3S)-6-carbamimidamido-1-chloro-2-oxohexan-3-yl]-L-phenylalaninamide × 1 CA CALCIUM ION × 6 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；15 % PEG 8000 100 MM ZINC ACETATE 100 MM SODIUM CACODYLATE, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.00 Å R-free 0.207

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 1CVR Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4IEF Complex of Porphyromonas gingivalis RgpB pro- and mature domains Deposited 2012-12-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 25–229（205 aa）
Chain B 230–662（433 aa） Fragment：UNP residues 230-662
Non-standard monomer：Yes (specific site not provided by mmCIF) CL CHLORIDE ION × 1 BA BARIUM ION × 1 CA CALCIUM ION × 4 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；14% polyethylene glycol 6000, 0.1M sodium acetate, 0.2M calcium chloride, 0.01 M barium chloride, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.30 Å R-free 0.225
4IEF Complex of Porphyromonas gingivalis RgpB pro- and mature domains Deposited 2012-12-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 25–229（205 aa）
Chain D 230–662（433 aa） Fragment：UNP residues 230-662
Non-standard monomer：Yes (specific site not provided by mmCIF) BA BARIUM ION × 1 CA CALCIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；14% polyethylene glycol 6000, 0.1M sodium acetate, 0.2M calcium chloride, 0.01 M barium chloride, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.30 Å R-free 0.225
4IEF Complex of Porphyromonas gingivalis RgpB pro- and mature domains Deposited 2012-12-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 25–229（205 aa）
Chain F 230–662（433 aa） Fragment：UNP residues 230-662
Non-standard monomer：Yes (specific site not provided by mmCIF) BA BARIUM ION × 1 CA CALCIUM ION × 4 NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；14% polyethylene glycol 6000, 0.1M sodium acetate, 0.2M calcium chloride, 0.01 M barium chloride, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.30 Å R-free 0.225
4IEF Complex of Porphyromonas gingivalis RgpB pro- and mature domains Deposited 2012-12-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain G 25–229（205 aa）
Chain H 230–662（433 aa） Fragment：UNP residues 230-662
Non-standard monomer：Yes (specific site not provided by mmCIF) BA BARIUM ION × 1 CA CALCIUM ION × 3 MG MAGNESIUM ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；14% polyethylene glycol 6000, 0.1M sodium acetate, 0.2M calcium chloride, 0.01 M barium chloride, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.30 Å R-free 0.225
5AG8 CRYSTAL STRUCTURE OF A MUTANT (665I6H) OF THE C-TERMINAL DOMAIN OF RGPB Deposited 2015-01-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 577–736（160 aa） Fragment：IGSF AND CTD DOMAINS, RESIDUES 577-736
Not recorded SO4 SULFATE ION × 3 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions 30% PEG 4000, 0.2M (NH4)2SO4, 10% PEG 300
Resolution 1.90 Å R-free 0.202
5AG8 CRYSTAL STRUCTURE OF A MUTANT (665I6H) OF THE C-TERMINAL DOMAIN OF RGPB Deposited 2015-01-29 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 577–736（160 aa） Fragment：IGSF AND CTD DOMAINS, RESIDUES 577-736
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions 30% PEG 4000, 0.2M (NH4)2SO4, 10% PEG 300
Resolution 1.90 Å R-free 0.202
5AG9 CRYSTAL STRUCTURE OF A MUTANT (665sXa) C-TERMINAL DOMAIN OF RGPB Deposited 2015-01-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 577–736（160 aa） Fragment：IGSF AND CTD DOMAINS, RESIDUES 577-736
Mutation：YES SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions 30% PEG 4000,0.2 M (NH4)2SO4
Resolution 2.11 Å R-free 0.254
5AG9 CRYSTAL STRUCTURE OF A MUTANT (665sXa) C-TERMINAL DOMAIN OF RGPB Deposited 2015-01-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 577–736（160 aa） Fragment：IGSF AND CTD DOMAINS, RESIDUES 577-736
Mutation：YES SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions 30% PEG 4000,0.2 M (NH4)2SO4
Resolution 2.11 Å R-free 0.254
5HFS CRYSTAL STRUCTURE OF C-TERMINAL DOMAIN OF CARGO PROTEINS OF TYPE IX SECRETION SYSTEM Deposited 2016-01-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 665–736（72 aa）
Chain B 665–736（72 aa）
Not recorded CA CALCIUM ION × 1 ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.4；277 K；PEG 3350, Lithium sulphate, Bis Tris
Resolution 1.97 Å R-free 0.247

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

View Construct and Data Evidence
UniProt name CPG2_PORGI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–435； UniProt 230–664

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 1cvr

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1cvr
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1cvr
Deposition date deposition_date1999-08-24
Structure title titleCrystal structure of the Arg specific cysteine proteinase gingipain R (RGPB)
Keywords keywordsCASPASES, CYSTEINE PROTEINASE, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION
▼

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

Radius of gyration Rg (Guinier) rg_guinier22.28 Å
Radius of gyration Rg (electron density) rg_electron21.21 Å
Forward intensity I(0) i039786400.00
Molecular weight molecular_weight48440.0 kDa
Excluded volume excluded_volume60396 ų
Envelope volume envelope_volume68544 ų
Hydration-shell volume shell_volume26283 ų
Envelope diameter envelope_diameter76.3 Å
Shell Rg shell_rg28.88 Å
Envelope Rg envelope_rg21.61 Å
Shape Rg shape_rg21.19 Å
Total Rg total_rg22.18 Å
Total atoms total_atoms3387
Residues n_residues432
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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 dmax71.9 Å
Rg (real space) rg_real22.19 Å
Rg uncertainty (real space) rg_real_error0.52 Å
I(0) (real space) i0_real3.9790e+07
I(0) uncertainty (real space) i0_real_error5.5150e+05
Rg (reciprocal space) rg_reciprocal22.22 Å
I(0) (reciprocal space) i0_reciprocal39790000.0000
Solution quality estimate total_estimate0.8075
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary28.3 Å
Skewness Skewness skewness0.271
Kurtosis Kurtosis kurtosis-0.230
Angular range angular_range— – 0.3550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9963000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.834; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (5)

▼

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1cvra1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.18 — E set domains
Family Family familyb.1.18.12 — Gingipain R (RgpB), C-terminal domain
Domain ID domain_idd1cvra2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.17 — Caspase-like
Superfamily Superfamily superfamilyc.17.1 — Caspase-like
Family Family familyc.17.1.2 — Gingipain R (RgpB), N-terminal domain

CATH v4.4 (3 domains)

Domain ID domain_id1cvrA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10390 — Gingipain r; domain 1
Domain ID domain_id1cvrA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily1460 —
Domain ID domain_id1cvrA03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
▶

8. Citations (1)

▶

9. Files and Curves (10)