SAXSdb — 5ag9

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

Gingipain R2

Porphyromonas gingivalis W83

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 577–736	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 577–736	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

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 5AG9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CVR Crystal structure of the Arg specific cysteine proteinase gingipain R (RGPB) Deposited 1999-08-24	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 230–664（435 aa）	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
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 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	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 mutation/modification 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
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 8 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 3–162； UniProt 577–736 Author chain B； PDBConstruct 3–162； UniProt 577–736

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5ag9
Deposition date deposition_date	2015-01-29
Structure title title	CRYSTAL STRUCTURE OF A MUTANT (665sXa) C-TERMINAL DOMAIN OF RGPB
Keywords keywords	HYDROLASE, TYPE IX SECRETION SYSTEM; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	26.71 Å
Radius of gyration Rg (electron density) rg_electron	26.56 Å
Forward intensity I(0) i0	18104800.00
Molecular weight molecular_weight	31999.0 kDa
Excluded volume excluded_volume	40052 Å³
Envelope volume envelope_volume	52599 Å³
Hydration-shell volume shell_volume	18846 Å³
Envelope diameter envelope_diameter	97.5 Å
Shell Rg shell_rg	30.02 Å
Envelope Rg envelope_rg	26.73 Å
Shape Rg shape_rg	26.56 Å
Total Rg total_rg	27.00 Å
Total atoms total_atoms	2233
Residues n_residues	298
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	94.1 Å
Rg (real space) rg_real	27.11 Å
Rg uncertainty (real space) rg_real_error	0.83 Å
I(0) (real space) i0_real	1.8100e+07
I(0) uncertainty (real space) i0_real_error	2.7690e+05
Rg (reciprocal space) rg_reciprocal	26.99 Å
I(0) (reciprocal space) i0_reciprocal	18100000.0000
Solution quality estimate total_estimate	0.7830
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.3 Å
Skewness Skewness skewness	0.609
Kurtosis Kurtosis kurtosis	-0.239
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3508000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.646; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.341; Smooth: 0.895

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Gingipain R2
Molecular weight formula_weight	17062.4 kDa
EC 编号 ec_number	3.4.22.37
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2487

GPTLVPTKMQVTAPANISASAQTFEVACDYNGAIATLSDDGDMVGTAIVKDGKAIIKLNESIADETNLTLTVVGYNKVTVIKDVKVEGTSIEGRAADKPYTVAVSGKTITVESPAAGLTIFDMNGRRVATAKNRMVFEAQNGVYAVRIATEGKTYTEKVIVK

来源 Source

来源生物 organism	Porphyromonas gingivalis W83
NCBI Class编号 ncbi_taxonomy_id	242619
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	254

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5ag9A01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5ag9B01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	51.570 Å
Unit-cell length b length_b	61.810 Å
Unit-cell length c length_c	54.050 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	116.79 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.110 Å
Low-resolution limit resolution_low	48.250 Å
R factor r_factor	0.1954
R_work r_work	0.1922
R_free r_free	0.2541

fit	/app/data/saxs_computation/ag/5ag9/5ag9.fit
pddf	/app/data/pr_computation/ag/5ag9/5ag9.pr.out
profile	/app/data/saxs_computation/ag/5ag9/5ag9.dat

CRYSTAL STRUCTURE OF A MUTANT (665sXa) C-TERMINAL DOMAIN OF RGPB

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

Gingipain R2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction