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- PDB-4ief: Complex of Porphyromonas gingivalis RgpB pro- and mature domains -

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Basic information

Entry
Database: PDB / ID: 4ief
TitleComplex of Porphyromonas gingivalis RgpB pro- and mature domains
Components(Gingipain R2 ...) x 2
KeywordsHYDROLASE / alpha/beta/alpha sandwich / cysteine endopeptidase
Function / homology
Function and homology information


gingipain R / calcium-dependent cysteine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular region
Similarity search - Function
Immunoglobulin-like - #3800 / Gingipain r; domain 1 / Peptidase M60, C-terminal / Peptidase M60 C-terminal domain / Peptidase C25, Ig-like domain / Gingipain propeptide / Gingipain, N-terminal superfamily / Gingipain propeptide superfamily / Gingipain, N-terminal / Peptidase family C25, C terminal ig-like domain ...Immunoglobulin-like - #3800 / Gingipain r; domain 1 / Peptidase M60, C-terminal / Peptidase M60 C-terminal domain / Peptidase C25, Ig-like domain / Gingipain propeptide / Gingipain, N-terminal superfamily / Gingipain propeptide superfamily / Gingipain, N-terminal / Peptidase family C25, C terminal ig-like domain / Propeptide_C25 / Gingipain / Peptidase family C25 / Secretion system C-terminal sorting domain / Rossmann fold - #1460 / Caspase-like domain superfamily / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
Authorsde Diego, I. / Veillard, F.T. / Guevara, T. / Potempa, B. / Sztukowska, M. / Potempa, J. / Gomis-Ruth, F.X.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Porphyromonas gingivalis Virulence Factor Gingipain RgpB Shows a Unique Zymogenic Mechanism for Cysteine Peptidases.
Authors: de Diego, I. / Veillard, F.T. / Guevara, T. / Potempa, B. / Sztukowska, M. / Potempa, J. / Gomis-Ruth, F.X.
History
DepositionDec 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Mar 29, 2017Group: Refinement description
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gingipain R2 Pro-Domain
B: Gingipain R2 Mature Domain
C: Gingipain R2 Pro-Domain
D: Gingipain R2 Mature Domain
E: Gingipain R2 Pro-Domain
F: Gingipain R2 Mature Domain
G: Gingipain R2 Pro-Domain
H: Gingipain R2 Mature Domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)288,87333
Polymers287,4198
Non-polymers1,45325
Water15,457858
1
A: Gingipain R2 Pro-Domain
B: Gingipain R2 Mature Domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3109
Polymers71,8552
Non-polymers4557
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-61 kcal/mol
Surface area24030 Å2
MethodPISA
2
C: Gingipain R2 Pro-Domain
D: Gingipain R2 Mature Domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1126
Polymers71,8552
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-46 kcal/mol
Surface area23550 Å2
MethodPISA
3
E: Gingipain R2 Pro-Domain
F: Gingipain R2 Mature Domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,22110
Polymers71,8552
Non-polymers3678
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-63 kcal/mol
Surface area23640 Å2
MethodPISA
4
G: Gingipain R2 Pro-Domain
H: Gingipain R2 Mature Domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2298
Polymers71,8552
Non-polymers3746
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-65 kcal/mol
Surface area23630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.420, 133.140, 109.830
Angle α, β, γ (deg.)90.00, 90.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Gingipain R2 ... , 2 types, 8 molecules ACEGBDFH

#1: Protein
Gingipain R2 Pro-Domain / Arg-gingipain / Gingipain 2 / RGP-2


Mass: 23226.334 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: PG_0506, prtRII, rgp2, rgpB / Production host: Escherichia coli (E. coli) / References: UniProt: P95493
#2: Protein
Gingipain R2 Mature Domain / Arg-gingipain / Gingipain 2 / RGP-2


Mass: 48628.512 Da / Num. of mol.: 4 / Fragment: UNP residues 230-662
Source method: isolated from a genetically manipulated source
Details: modified rgpB gene / Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: PG_0506, prtRII, rgp2, rgpB / Production host: Escherichia coli (E. coli) / References: UniProt: P95493, gingipain R

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Non-polymers , 8 types, 883 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ba
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 858 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 31, 2012 / Details: mirrors
RadiationMonochromator: channel-cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.3→47.3 Å / Num. obs: 106820 / % possible obs: 99.1 % / Observed criterion σ(F): 106820 / Observed criterion σ(I): 2.6 / Biso Wilson estimate: 41.37 Å2 / Rmerge(I) obs: 0.07
Reflection shellResolution: 2.3→2.36 Å / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.64 / % possible all: 91.2

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
BUSTER2.11.2refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1CVR

1cvr


Resolution: 2.3→33.67 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.9089 / SU R Cruickshank DPI: 0.378 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2247 5323 4.98 %RANDOM
Rwork0.1893 ---
all0.191 ---
obs0.191 106784 99.25 %-
Displacement parametersBiso mean: 39.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.1917 Å20 Å2-0.2361 Å2
2--2.2839 Å20 Å2
3----1.0922 Å2
Refine analyzeLuzzati coordinate error obs: 0.299 Å
Refinement stepCycle: LAST / Resolution: 2.3→33.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19151 0 37 858 20046
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00819511HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0426452HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d9085SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes567HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2767HARMONIC5
X-RAY DIFFRACTIONt_it19511HARMONIC20
X-RAY DIFFRACTIONt_nbd52SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.99
X-RAY DIFFRACTIONt_other_torsion2.92
X-RAY DIFFRACTIONt_chiral_improper_torsion2669SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact22075SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2391 361 4.94 %
Rwork0.211 6952 -
all0.2123 7313 -
obs--99.25 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6181-0.09310.19731.2083-0.18120.36190.05140.0026-0.13720.0556-0.0194-0.28810.11270.1449-0.032-0.09190.0067-0.001-0.14270.00790.047712.4526-56.14311.3429
21.16550.61120.00991.5403-0.16090.703-0.0685-0.0326-0.17280.0125-0.013-0.174-0.06360.02270.0815-0.0962-0.0013-0.0056-0.14110.0367-0.00245.2045-27.322616.8804
32.72010.23820.57881.1455-0.11411.17830.0211-0.09590.04330.1431-0.0653-0.2348-0.00980.06080.0442-0.0129-0.0617-0.1463-0.06520.0874-0.006326.2441-14.72734.1008
42.86460.43180.021.18180.390.7892-0.2911-0.04510.5355-0.11740.10250.0126-0.26840.07470.1886-0.02580.0111-0.1041-0.18470.0215-0.036226.555547.07417.8427
51.55030.40880.20661.9675-0.18250.9145-0.0064-0.12640.00120.06660.014-0.1511-0.0031-0.007-0.0076-0.1010.0152-0.0203-0.1326-0.0291-0.071233.107818.39212.57
63.1799-0.5008-1.17320.2215-0.36411.64610.0395-0.33940.04490.27120.02210.2824-0.21490.0382-0.06160.079-0.06290.0833-0.058-0.0196-0.082415.79027.855934.4979
70.75980.01910.47672.47270.18650.7533-0.12320.13410.3305-0.33320.1161-0.0786-0.2296-0.00540.007-0.1289-0.0594-0.0509-0.08140.0860.009368.61247.561950.8285
81.43850.3560.40351.63360.65051.3451-0.0026-0.0078-0.03360.09990.0052-0.089-0.03090.0234-0.0026-0.13660.0282-0.0237-0.08330.0424-0.090164.112-21.022758.9969
91.4093-0.39070.34031.93630.47622.54450.01850.12130.0293-0.283-0.02290.23340.1742-0.16820.0044-0.10280.0204-0.0879-0.00550.01040.024542.132-32.442.1605
100.47290.56430.13681.82930.78881.9120.0303-0.1023-0.23450.32690.1071-0.35220.3395-0.0856-0.1373-0.15890.0266-0.0342-0.1190.05720.093565.9689-95.627235.7028
111.20690.178-0.07351.34070.21181.0519-0.0331-0.0885-0.11350.0080.0732-0.10260.0315-0.1072-0.0401-0.1409-0.040.0092-0.10410.0596-0.014459.0845-66.610730.7506
121.2583-0.06140.06762.65591.16213.2028-0.0069-0.1827-0.05180.29390.00770.0202-0.0475-0.1462-0.0008-0.08320.01870.07080.00250.0763-0.064443.2448-54.957753.3941
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|31 - A|227 }A31 - 227
2X-RAY DIFFRACTION2{ B|239 - B|580 }B239 - 580
3X-RAY DIFFRACTION3{ B|581 - B|661 }B581 - 661
4X-RAY DIFFRACTION4{ C|30 - C|229 }C30 - 229
5X-RAY DIFFRACTION5{ D|238 - D|580 }D238 - 580
6X-RAY DIFFRACTION6{ D|581 - D|661 }D581 - 661
7X-RAY DIFFRACTION7{ E|30 - E|228 }E30 - 228
8X-RAY DIFFRACTION8{ F|238 - F|580 }F238 - 580
9X-RAY DIFFRACTION9{ F|581 - F|661 }F581 - 661
10X-RAY DIFFRACTION10{ G|31 - G|226 }G31 - 226
11X-RAY DIFFRACTION11{ H|238 - H|580 }H238 - 580
12X-RAY DIFFRACTION12{ H|581 - H|661 }H581 - 661

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