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- PDB-5ag9: CRYSTAL STRUCTURE OF A MUTANT (665sXa) C-TERMINAL DOMAIN OF RGPB -

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Basic information

Entry
Database: PDB / ID: 5ag9
TitleCRYSTAL STRUCTURE OF A MUTANT (665sXa) C-TERMINAL DOMAIN OF RGPB
ComponentsGingipain R2
KeywordsHYDROLASE / TYPE IX SECRETION SYSTEM
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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPorphyromonas gingivalis W83 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
Authorsde Diego, I. / Ksiazek, M. / Mizgalska, D. / Golik, P. / Szmigielski, B. / Nowak, M. / Nowakowska, Z. / Potempa, B. / Koneru, L. / Nguyen, K.A. ...de Diego, I. / Ksiazek, M. / Mizgalska, D. / Golik, P. / Szmigielski, B. / Nowak, M. / Nowakowska, Z. / Potempa, B. / Koneru, L. / Nguyen, K.A. / Enghild, J. / Thogersen, I.B. / Dubin, G. / Gomis-Ruth, F.X. / 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. / Thogersen, 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. / Thogersen, I.B. / Gao, J. / Kwan, A.H. / Trewhella, J. / Dubin, G. / Gomis-Ruth, F.X. / Nguyen, K.A. / Potempa, J.
History
DepositionJan 29, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_name_com / entity_src_gen / entity_src_nat / struct_ref
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity.pdbx_description / _entity.src_method / _entity_name_com.name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,6057
Polymers34,1252
Non-polymers4805
Water4,576254
1
A: Gingipain R2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2553
Polymers17,0621
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Gingipain R2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3514
Polymers17,0621
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.570, 61.810, 54.050
Angle α, β, γ (deg.)90.00, 116.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 17062.449 Da / Num. of mol.: 2 / Fragment: IGSF AND CTD DOMAINS, RESIDUES 577-736 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: FACTOR XA CLEAVAGE SITE SUBSTITUTING RESIDUES 665-669
Source: (gene. exp.) Porphyromonas gingivalis W83 (bacteria)
Gene: rgpB, prtRII, rgp2, PG_0506 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P95493, gingipain R
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFACTOR XA CLEAVAGE SITE (IEGRAA) SUBSTITUTES RESIDUES 665- 670 FIRST TWO RESIDUES REMANENT OF ...FACTOR XA CLEAVAGE SITE (IEGRAA) SUBSTITUTES RESIDUES 665- 670 FIRST TWO RESIDUES REMANENT OF ENGINEERED 3C PROTEASE CLEAVAGE SITE

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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: 2.44 Å3/Da / Density % sol: 49.7 % / Description: NONE
Crystal growDetails: 30% PEG 4000,0.2 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.11→38.03 Å / Num. obs: 17553 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 6.4
Reflection shellResolution: 2.11→2.22 Å / Redundancy: 4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5AG8

5ag8


Resolution: 2.11→48.25 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.884 / SU B: 5.955 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.251 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. RESIDUES 663-671 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.2541 888 5.1 %RANDOM
Rwork0.19218 ---
obs0.19538 16650 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.591 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å20.3 Å2
2---0.73 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.11→48.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2208 0 25 254 2487
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022248
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9241.9743050
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8215294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.20125.89778
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.82615396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.075158
X-RAY DIFFRACTIONr_chiral_restr0.1280.2387
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211586
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.11→2.165 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 59 -
Rwork0.203 1167 -
obs--100 %

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