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- PDB-5hfs: CRYSTAL STRUCTURE OF C-TERMINAL DOMAIN OF CARGO PROTEINS OF TYPE ... -

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Basic information

Entry
Database: PDB / ID: 5hfs
TitleCRYSTAL STRUCTURE OF C-TERMINAL DOMAIN OF CARGO PROTEINS OF TYPE IX SECRETION SYSTEM
ComponentsGingipain R2
KeywordsHYDROLASE / Ig-like domain / TYPE IX SECRETION SYSTEM / protease
Function / homology
Function and homology information


gingipain R / calcium-dependent cysteine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular region
Similarity search - Function
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 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 / Caspase-like domain superfamily / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsGolik, P. / Szmigielski, B. / Ksiazek, M. / Nowakowska, Z. / Mizgalska, D. / Nowak, M. / Dubin, G. / Potempa, J.
CitationJournal: Sci Rep / Year: 2016
Title: The outer-membrane export signal of Porphyromonas gingivalis type IX secretion system (T9SS) is a conserved C-terminal beta-sandwich domain.
Authors: de Diego, I. / Ksiazek, M. / Mizgalska, D. / Koneru, L. / Golik, P. / Szmigielski, B. / Nowak, M. / Nowakowska, Z. / Potempa, B. / Houston, J.A. / Enghild, J.J. / Thgersen, I.B. / Gao, J. / ...Authors: de Diego, I. / Ksiazek, M. / Mizgalska, D. / Koneru, L. / Golik, P. / Szmigielski, B. / Nowak, M. / Nowakowska, Z. / Potempa, B. / Houston, J.A. / Enghild, J.J. / Thgersen, I.B. / Gao, J. / Kwan, A.H. / Trewhella, J. / Dubin, G. / Gomis-Ruth, F.X. / Nguyen, K.A. / Potempa, J.
History
DepositionJan 7, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gingipain R2
B: Gingipain R2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8838
Polymers15,5162
Non-polymers3676
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-86 kcal/mol
Surface area7570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.690, 37.690, 184.150
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 7757.896 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: rgpB, prtRII, rgp2, PG_0506 / Production host: Escherichia coli (E. coli) / References: UniProt: P95493, gingipain R
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.4 / Details: PEG 3350, Lithium sulphate, Bis Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.97→32.64 Å / Num. obs: 10503 / % possible obs: 99.98 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 7
Reflection shellResolution: 1.97→2.08 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CVR

1cvr


Resolution: 1.97→32.64 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 32.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.247 546 5.25 %
Rwork0.219 --
obs0.2206 10402 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→32.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms944 0 6 33 983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007956
X-RAY DIFFRACTIONf_angle_d1.1181299
X-RAY DIFFRACTIONf_dihedral_angle_d11.598333
X-RAY DIFFRACTIONf_chiral_restr0.039163
X-RAY DIFFRACTIONf_plane_restr0.003162
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.969-2.16710.35091240.2452472X-RAY DIFFRACTION100
2.1671-2.48060.27341390.24842460X-RAY DIFFRACTION100
2.4806-3.12490.29011530.26182478X-RAY DIFFRACTION100
3.1249-32.6450.20441300.18942446X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 0.5386 Å / Origin y: 4.4382 Å / Origin z: -6.5625 Å
111213212223313233
T0.1808 Å2-0.0007 Å2-0.0109 Å2-0.1633 Å2-0.004 Å2--0.1747 Å2
L6.1716 °20.3667 °2-0.9884 °2-0.699 °2-0.0045 °2--1.3914 °2
S-0.3137 Å °0.0057 Å °0.0334 Å °-0.0158 Å °0.1126 Å °-0.0365 Å °-0.0458 Å °0.0242 Å °0.1838 Å °
Refinement TLS groupSelection details: all

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