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- PDB-6i0x: Porphyromonas gingivalis peptidylarginine deminase (PPAD) mutant ... -

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Basic information

Entry
Database: PDB / ID: 6i0x
TitlePorphyromonas gingivalis peptidylarginine deminase (PPAD) mutant G231N/E232T/N235D in complex with Cl-amidine.
ComponentsPeptidylarginine deiminase
KeywordsHYDROLASE / citrullination / odontopathogenic virulence factor / arginine demininase / periodontal disease / rheumatoid arthitis
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amidines / agmatine deiminase activity / putrescine biosynthetic process / protein-arginine deiminase activity / extracellular region
Similarity search - Function
Peptidyl-arginine deiminase, Porphyromonas-type / Porphyromonas-type peptidyl-arginine deiminase / L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / Alpha Beta
Similarity search - Domain/homology
Chem-BFB / Peptidylarginine deiminase
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGomis-Ruth, F.X. / Goulas, T. / Sola, M. / Potempa, J.
Citation
Journal: Protein Sci. / Year: 2019
Title: Structure, function, and inhibition of a genomic/clinical variant of Porphyromonas gingivalis peptidylarginine deiminase.
Authors: Bereta, G. / Goulas, T. / Madej, M. / Bielecka, E. / Sola, M. / Potempa, J. / Xavier Gomis-Ruth, F.
#1: Journal: Sci Rep / Year: 2015
Title: Structure and mechanism of a bacterial host-protein citrullinating virulence factor, Porphyromonas gingivalis peptidylarginine deiminase.
Authors: Goulas, T. / Mizgalska, D. / Garcia-Ferrer, I. / Kantyka, T. / Guevara, T. / Szmigielski, B. / Sroka, A. / Millan, C. / Uson, I. / Veillard, F. / Potempa, B. / Mydel, P. / Sola, M. / ...Authors: Goulas, T. / Mizgalska, D. / Garcia-Ferrer, I. / Kantyka, T. / Guevara, T. / Szmigielski, B. / Sroka, A. / Millan, C. / Uson, I. / Veillard, F. / Potempa, B. / Mydel, P. / Sola, M. / Potempa, J. / Gomis-Ruth, F.X.
History
DepositionOct 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.2Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.3Jan 24, 2024Group: 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_conn_type
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _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_symmetry / _struct_conn_type.id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidylarginine deiminase
B: Peptidylarginine deiminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,27312
Polymers98,1912
Non-polymers1,08210
Water20,6271145
1
A: Peptidylarginine deiminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6947
Polymers49,0961
Non-polymers5996
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidylarginine deiminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5795
Polymers49,0961
Non-polymers4844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.840, 71.870, 104.720
Angle α, β, γ (deg.)90.00, 95.86, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Peptidylarginine deiminase


Mass: 49095.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The present is a triple point mutant G231N/E232T/N235D. In addition, catalytic cysteine C351 is covalently modified by the inhibitor Cl-amidine resulting in new residue CYA.
Source: (gene. exp.) Porphyromonas gingivalis (strain ATCC BAA-308 / W83) (bacteria)
Strain: ATCC BAA-308 / W83 / Gene: PG_1424 / Production host: Porphyromonas gingivalis (bacteria)
References: UniProt: Q9RQJ2, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amidines
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-BFB / N-[(1S)-1-(AMINOCARBONYL)-4-(ETHANIMIDOYLAMINO)BUTYL]BENZAMIDE / (S)-N-ALPHA-BENZOYL-N5-(2-FLUORO-1-IMINOETHYL)-L-ORNITHINE AMIDE


Mass: 276.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N4O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1145 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM sodium acetate, 15% [w/v] polyethylene glycol 3,350, pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979294 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979294 Å / Relative weight: 1
ReflectionResolution: 1.6→62.1 Å / Num. obs: 119834 / % possible obs: 98.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 11.1
Reflection shellResolution: 1.6→1.7 Å / Rmerge(I) obs: 0.562

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YTB

4ytb


Resolution: 1.6→62.08 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.093 / SU Rfree Blow DPI: 0.083 / SU Rfree Cruickshank DPI: 0.079
RfactorNum. reflection% reflectionSelection details
Rfree0.193 814 0.0068 %RANDOM
Rwork0.18 ---
obs0.18 119833 99.4 %-
Displacement parametersBiso mean: 24.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.7211 Å20 Å20.466 Å2
2--2.4918 Å20 Å2
3----1.7706 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: 1 / Resolution: 1.6→62.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6635 0 85 1145 7865
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016914HARMONIC2
X-RAY DIFFRACTIONt_angle_deg19406HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3103SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1188HARMONIC5
X-RAY DIFFRACTIONt_it6914HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.14
X-RAY DIFFRACTIONt_other_torsion2.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion899SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies4HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9034SEMIHARMONIC4
LS refinement shellResolution: 1.6→1.64 Å
RfactorNum. reflection% reflection
Rfree0.2488 -0.0063 %
Rwork0.2489 8546 -
obs--97.21 %
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)
10.3808-0.0113-0.04850.54650.00080.28530.0094-0.017-0.0187-0.0129-0.0086-0.00470.00610.0187-0.00090.0457-0.00410.027-0.0710.0035-0.0465-29.5631-23.309548.0786
21.2402-0.424-0.39040.96840.10840.80320.02940.11940.1536-0.0578-0.0217-0.1577-0.01690.0955-0.00780.02150.0010.049-0.06420.0158-0.027-10.6164-5.504935.4451
30.2972-0.06460.00590.37890.05870.60990.0094-0.0053-0.0332-0.1120.00920.03090.0566-0.0483-0.01860.1735-0.0033-0.0084-0.1352-0.0006-0.1163-37.2474-32.614.8234
40.99940.1053-0.33571.5372-0.16810.9440.0194-0.13570.0402-0.0698-0.00220.3327-0.0718-0.1743-0.01720.04320.00720.0012-0.0717-0.0047-0.0666-55.1194-14.851219.6385
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|44 - 359 A|501 - 501}
2X-RAY DIFFRACTION2{A|360 - 463}
3X-RAY DIFFRACTION3{B|44 - 359 B|501 - 501}
4X-RAY DIFFRACTION4{B|360 - 465}

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