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- PDB-4yt9: Crystal structure of Porphyromonas gingivalis peptidylarginine de... -

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Basic information

Entry
Database: PDB / ID: 4yt9
TitleCrystal structure of Porphyromonas gingivalis peptidylarginine deiminase (PPAD) substrate-unbound.
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
Peptidylarginine deiminase
Similarity search - Component
Biological speciesPorphyromonas gingivalis W83 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.5 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 15, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidylarginine deiminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2329
Polymers48,5641
Non-polymers6688
Water8,287460
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-17 kcal/mol
Surface area16970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.560, 60.300, 113.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidylarginine deiminase


Mass: 48564.223 Da / Num. of mol.: 1 / Fragment: UNP residues 44-475 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis W83 (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.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / 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

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.88 % / Description: Bar shaped.
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 100mM sodium acetate (pH4.5), 25% [w/v] polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.5→42.01 Å / Num. obs: 64233 / % possible obs: 98.5 % / Redundancy: 4.5 % / Biso Wilson estimate: 19.68 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 21
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 7.4 / Num. unique all: 9862 / % possible all: 95.7

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
XSCALEdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.5→42.01 Å / Cor.coef. Fo:Fc: 0.9662 / Cor.coef. Fo:Fc free: 0.9608 / SU R Cruickshank DPI: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.071 / SU Rfree Blow DPI: 0.068 / SU Rfree Cruickshank DPI: 0.066
RfactorNum. reflection% reflectionSelection details
Rfree0.1771 772 1.2 %RANDOM
Rwork0.1569 ---
obs0.1571 64233 98.52 %-
Displacement parametersBiso mean: 24.44 Å2
Baniso -1Baniso -2Baniso -3
1--2.294 Å20 Å20 Å2
2--2.7945 Å20 Å2
3----0.5005 Å2
Refine analyzeLuzzati coordinate error obs: 0.158 Å
Refinement stepCycle: 1 / Resolution: 1.5→42.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3358 0 65 460 3883
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013513HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.034766HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1580SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes94HARMONIC2
X-RAY DIFFRACTIONt_gen_planes510HARMONIC5
X-RAY DIFFRACTIONt_it3513HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.5
X-RAY DIFFRACTIONt_other_torsion2.67
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion451SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies6HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4572SEMIHARMONIC4
LS refinement shellResolution: 1.5→1.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2469 55 1.27 %
Rwork0.1783 4289 -
all0.1792 4344 -
obs--98.52 %
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)
10.4687-0.01170.01140.97990.02420.3974-0.0095-0.07280.00580.0679-0.0010.1272-0.0237-0.08390.0105-0.03470.00720.0064-0.0376-0.0021-0.031319.865835.158337.4495
20.8076-0.19510.5892.7458-0.27870.3003-0.0313-0.1957-0.1550.31720.1160.29740.0472-0.159-0.08480.0123-0.01730.0839-0.0010.0652-0.03514.060418.58651.9995
31.2007-0.1703-0.93920.79040.50562.97680.0727-0.1377-0.14310.02010.0266-0.1682-0.12760.3717-0.0994-0.0565-0.0277-0.0226-0.0155-0.0001-0.022747.707230.841238.8953
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|44 - 70 A|125 - 359 A|996 - 999}
2X-RAY DIFFRACTION2{A|71 - 124}
3X-RAY DIFFRACTION3{A|360 - 464 A|995 - 995}

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