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

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Basic information

Entry
Database: PDB / ID: 4ytb
TitleCrystal structure of Porphyromonas gingivalis peptidylarginine deiminase (PPAD) in complex with dipeptide Asp-Gln.
ComponentsPeptidylarginine deiminaseProtein-arginine deiminase
KeywordsHYDROLASE / Peptidylarginine deiminase / citrullination
Function / homology
Function and homology information


Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amidines / 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
ASPARTIC ACID / AZIDE ION / GLUTAMINE / IMIDAZOLE / PHOSPHATE ION / Peptidylarginine deiminase
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 2.0Mar 7, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Source and taxonomy
Category: atom_site / pdbx_distant_solvent_atoms ...atom_site / pdbx_distant_solvent_atoms / pdbx_entity_src_syn / pdbx_struct_conn_angle / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.occupancy / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_ligand_distance / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Jan 10, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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)49,43715
Polymers48,2371
Non-polymers1,20014
Water12,394688
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-42 kcal/mol
Surface area17430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.534, 71.306, 105.664
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Peptidylarginine deiminase / Protein-arginine deiminase


Mass: 48236.770 Da / Num. of mol.: 1 / Fragment: residues 44-475 / Source method: isolated from a natural source / Source: (natural) Porphyromonas gingivalis (bacteria)
References: UniProt: Q9RQJ2, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amidines

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Non-polymers , 9 types, 702 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ASP / ASPARTIC ACID / Aspartic acid


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4
#4: Chemical ChemComp-GLN / GLUTAMINE / Glutamine


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N2O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 688 / 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: 2.35 Å3/Da / Density % sol: 47.66 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100mM tri-sodium citrate, 2M ammonium sulfate, pH5.5-6.5
PH range: 5.5-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / 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: 1.4→46.15 Å / Num. obs: 90283 / % possible obs: 99.6 % / Redundancy: 12.6 % / Biso Wilson estimate: 14.22 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 36.3
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 8.5 / % possible all: 97.5

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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: 1.4→46.15 Å / Cor.coef. Fo:Fc: 0.9631 / Cor.coef. Fo:Fc free: 0.9742 / SU R Cruickshank DPI: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.053 / SU Rfree Blow DPI: 0.048 / SU Rfree Cruickshank DPI: 0.045
RfactorNum. reflection% reflectionSelection details
Rfree0.1492 903 1 %RANDOM
Rwork0.1456 ---
obs0.1456 90283 99.61 %-
Displacement parametersBiso mean: 17.35 Å2
Baniso -1Baniso -2Baniso -3
1-2.0782 Å20 Å20 Å2
2---1.9988 Å20 Å2
3----0.0794 Å2
Refine analyzeLuzzati coordinate error obs: 0.115 Å
Refinement stepCycle: 1 / Resolution: 1.4→46.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3424 0 53 689 4166
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013574HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.054878HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1628SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes99HARMONIC2
X-RAY DIFFRACTIONt_gen_planes531HARMONIC5
X-RAY DIFFRACTIONt_it3574HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion5.06
X-RAY DIFFRACTIONt_other_torsion2.65
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion465SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies15HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4908SEMIHARMONIC4
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.1816 65 1.04 %
Rwork0.1565 6204 -
all0.1567 6269 -
obs--99.61 %
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)
10.2273-0.0468-0.03750.36650.01580.25550.01190.0186-0.0009-0.0285-0.00390.02460.00240.0063-0.008-0.0054-0.0009-0.00040.0029-0.0018-0.0086-13.803913.4579-10.2203
20.29470.07840.05120.0425-0.10550.0679-0.00110.0096-0.01470.0019-0.00990.0250.06230.00320.0110.01680.01630.002-0.00960.0050.0038-12.2874-7.4049-5.8598
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|44 - 465 A|999 - 999}
2X-RAY DIFFRACTION2{A|502 - 503}

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