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- PDB-4ytg: Crystal structure of Porphyromonas gingivalis peptidylarginine de... -

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Basic information

Entry
Database: PDB / ID: 4ytg
TitleCrystal structure of Porphyromonas gingivalis peptidylarginine deiminase (PPAD) mutant C351A in complex with dipeptide Met-Arg.
ComponentsPeptidylarginine deiminase
KeywordsHYDROLASE / Peptidylarginine deiminase / citrullination
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
ARGININE / AZIDE ION / CYSTEINE / METHIONINE / Peptidylarginine deiminase
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGoulas, T. / Mizgalska, D. / Garcia-Ferrer, I. / Kantyka, T. / Guevara, T. / Szmigielski, B. / Sroka, A. / Millan, C. / Uson, I. / Veillard, F. ...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.
CitationJournal: 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
DepositionMar 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2Sep 26, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / entity_src_nat / Item: _entity.src_method
Revision 1.3Jan 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: Peptidylarginine deiminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,25313
Polymers48,2051
Non-polymers1,04912
Water7,674426
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-22 kcal/mol
Surface area16720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.360, 59.320, 84.610
Angle α, β, γ (deg.)90.00, 126.59, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Peptidylarginine deiminase


Mass: 48204.707 Da / Num. of mol.: 1 / Fragment: residues 44-475 / Mutation: C351A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (strain ATCC BAA-308 / W83) (bacteria)
Gene: PG_1424 / Production host: Porphyromonas gingivalis W83 (bacteria)
References: UniProt: Q9RQJ2, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amidines

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Non-polymers , 8 types, 438 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#4: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#5: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM tri-sodium citrate, 20% [w/v] polyethylene glycol 3,000, pH5.5-6.5
PH range: 5.5-6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→67.9 Å / Num. obs: 38882 / % possible obs: 99.3 % / Redundancy: 6.5 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 22.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 3.7 / Num. unique all: 5771 / CC1/2: 0.927 / % possible all: 98.9

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4yt9

4yt9


Resolution: 1.8→48.57 Å / Cor.coef. Fo:Fc: 0.9539 / Cor.coef. Fo:Fc free: 0.9473 / SU R Cruickshank DPI: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.118 / SU Rfree Blow DPI: 0.105 / SU Rfree Cruickshank DPI: 0.102
RfactorNum. reflection% reflectionSelection details
Rfree0.182 699 1.8 %RANDOM
Rwork0.1555 ---
obs0.156 38882 99.69 %-
Displacement parametersBiso mean: 28.64 Å2
Baniso -1Baniso -2Baniso -3
1-3.5006 Å20 Å27.126 Å2
2---0.5516 Å20 Å2
3----2.949 Å2
Refine analyzeLuzzati coordinate error obs: 0.192 Å
Refinement stepCycle: 1 / Resolution: 1.8→48.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3336 0 38 426 3800
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013453HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.994686HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1551SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes94HARMONIC2
X-RAY DIFFRACTIONt_gen_planes496HARMONIC5
X-RAY DIFFRACTIONt_it3453HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.07
X-RAY DIFFRACTIONt_other_torsion2.56
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion447SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies3HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4393SEMIHARMONIC4
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.265 52 1.74 %
Rwork0.2226 2940 -
all0.2233 2992 -
obs--99.69 %
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)
10.8336-0.1070.710.5818-0.21011.06530.03840.0062-0.0129-0.0228-0.07760.0301-0.0391-0.06190.0393-0.03340.0232-0.0059-0.0322-0.0155-0.010745.039349.726986.4719
20.2016-0.06920.009200.0556-0.05280.00260.0079-0.01980.02350.0017-0.01290.0239-0.008-0.00430.01820.019-0.0497-0.03090.01860.012955.733336.016396.7573
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|44 - 463 A|998 - 999}
2X-RAY DIFFRACTION2{L|1 - 2}

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