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- PDB-6ce1: Crystal structure of Peptidyl Arginine Deiminase Type III (PADI3) -

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Entry
Database: PDB / ID: 6ce1
TitleCrystal structure of Peptidyl Arginine Deiminase Type III (PADI3)
ComponentsProtein-arginine deiminase type-3
KeywordsHYDROLASE / Citrullination Calcium Follicle Hair Skin
Function / homology
Function and homology information


protein-arginine deiminase / protein-arginine deiminase activity / Chromatin modifying enzymes / intracellular membrane-bounded organelle / calcium ion binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Protein-arginine deiminase, central domain / Protein-arginine deiminase, N-terminal domain / Protein-arginine deiminase / Protein-arginine deiminase, C-terminal / Protein-arginine deiminase (PAD), N-terminal / Protein-arginine deiminase (PAD), central domain / Protein-arginine deiminase, central domain superfamily / PAD, N-terminal domain superfamily / Protein-arginine deiminase (PAD) / Protein-arginine deiminase (PAD) N-terminal domain ...Protein-arginine deiminase, central domain / Protein-arginine deiminase, N-terminal domain / Protein-arginine deiminase / Protein-arginine deiminase, C-terminal / Protein-arginine deiminase (PAD), N-terminal / Protein-arginine deiminase (PAD), central domain / Protein-arginine deiminase, central domain superfamily / PAD, N-terminal domain superfamily / Protein-arginine deiminase (PAD) / Protein-arginine deiminase (PAD) N-terminal domain / Protein-arginine deiminase (PAD) middle domain / L-arginine/glycine Amidinotransferase; Chain A / 5-stranded Propeller / L-arginine/glycine Amidinotransferase; Chain A / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Protein-arginine deiminase type-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRechiche, O. / Lee, T.V. / Lott, J.S.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
New Zealand Wool Industry Research LimitedA18223 New Zealand
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Structural characterization of human peptidyl-arginine deiminase type III by X-ray crystallography
Authors: Rechiche, O. / Lee, T.V. / Lott, J.S.
History
DepositionFeb 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2019Provider: repository / Type: Initial release
Revision 2.0May 19, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Source and taxonomy
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / diffrn / entity_src_gen / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_conf / struct_sheet_range
Item: _diffrn.pdbx_serial_crystal_experiment / _entity_src_gen.pdbx_host_org_strain ..._diffrn.pdbx_serial_crystal_experiment / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_low / _software.version / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Polymer geometry
Details: We have refined the model using the last version of PHENIX 1.19.2-4158 and obtained a model with better geometry.
Provider: author / Type: Coordinate replacement
Revision 2.1Oct 6, 2021Group: Database references / Category: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 13, 2021Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 2.3Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-arginine deiminase type-3


Theoretical massNumber of molelcules
Total (without water)77,5301
Polymers77,5301
Non-polymers00
Water00
1
A: Protein-arginine deiminase type-3

A: Protein-arginine deiminase type-3


Theoretical massNumber of molelcules
Total (without water)155,0602
Polymers155,0602
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area4860 Å2
ΔGint-32 kcal/mol
Surface area50450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.023, 115.023, 328.487
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

#1: Protein Protein-arginine deiminase type-3 / Peptidylarginine deiminase III / Protein-arginine deiminase type III


Mass: 77530.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: chemically synthesized gene / Source: (gene. exp.) Homo sapiens (human) / Gene: PADI3, PAD3, PDI3 / Plasmid: PDEST17 / Details (production host): Gateway / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): pLysS / References: UniProt: Q9ULW8, protein-arginine deiminase

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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: 2.75 Å3/Da / Density % sol: 55.22 % / Description: Pyramidal shape
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Sodium HEPES + MOPS (acid) Ethylene glycols PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953694 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 7, 2017
RadiationMonochromator: silicon double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953694 Å / Relative weight: 1
ReflectionResolution: 2.8→49.24 Å / Num. obs: 21054 / % possible obs: 100 % / Redundancy: 18.6 % / Biso Wilson estimate: 66.14 Å2 / CC1/2: 0.993 / Rpim(I) all: 0.132 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) all% possible all
2.8-2.9517.50.830350.3342.16100
8.85-49.2417.431.67410.9980.01799.4

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Processing

Software
NameVersionClassification
phenix.refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHENIX1.13_2998phasing
Coot0.8.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DEW

2dew


Resolution: 2.8→49.24 Å / SU ML: 0.4273 / Cross valid method: FREE R-VALUE / Phase error: 29.4801
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2735 1032 4.91 %
Rwork0.2344 19978 -
obs0.2363 21010 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.07 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4253 0 0 0 4253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00394353
X-RAY DIFFRACTIONf_angle_d0.77595937
X-RAY DIFFRACTIONf_chiral_restr0.0519672
X-RAY DIFFRACTIONf_plane_restr0.0081786
X-RAY DIFFRACTIONf_dihedral_angle_d16.31431466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.950.35421550.33562769X-RAY DIFFRACTION98.95
2.95-3.130.3431360.30852837X-RAY DIFFRACTION99.87
3.13-3.370.33171610.27982809X-RAY DIFFRACTION99.87
3.37-3.710.28631430.22972820X-RAY DIFFRACTION99.97
3.71-4.250.26821380.222868X-RAY DIFFRACTION100
4.25-5.350.22131430.19462881X-RAY DIFFRACTION100
5.35-49.240.25771560.22812994X-RAY DIFFRACTION99.87
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)
14.41067726799-0.168276445427-2.14140475761.85456121394-0.1582010848473.74319341482-0.266858647964-0.188453058145-0.05754704163970.06086941162720.185260278434-0.03346174031550.07270550050750.1854759523490.0007218976104390.5436000835420.00797222792209-0.06063147461130.325630785489-0.01377527974760.3857288597883.0301793336-16.351373236541.0306259685
21.61632405178-0.286792589816-1.073627911930.6928828622560.6725775769215.503458519740.219291106690.3407275890370.230638381984-0.3796800300380.14463132891-0.0601666864797-0.4493910240460.494058225512-0.132595427930.5585741490570.02766871768380.1236215424530.731221325451-0.01782900757610.52819680224925.3383962726-19.095748630418.8981656883
32.10519349353-1.57210481288-0.882367254232.684826983630.1517821845817.358402899260.03013176039310.163752001385-0.655038526902-0.203632642322-0.267389520802-0.1434458268990.8095105763880.7140120805180.1956974049850.5272052503210.1121689233550.06496820263220.761103810805-0.08983312961910.56976799659226.1907810869-30.968341324317.4874529131
41.56296455510.990869361542-1.093199774961.35470833159-1.041833569832.89408966407-0.186371579151-0.42909046003-0.4340913236370.110734344826-0.153461166879-0.2336448127490.3030593528171.012514089120.4440074429450.5297332863140.2239455962010.0158204213470.938572247989-0.0116275801430.56303685299331.5495669593-23.632330963811.5865291291
57.835937651355.40998507239-1.142022765268.29300678503-0.06263237510650.853833750948-0.74877395834-0.701780535450.582787026477-0.1252329455980.212122476346-0.6921209353730.4563624369661.186961936360.1470362936120.9143254653030.241664394385-0.2260874532251.626555086050.2667579302190.68079510446249.3906757216-20.8354964107-12.42489523
64.18260721087-0.6234285607861.267855657813.32802428856-1.547453022411.005920617770.519842318276-0.226929029383-0.026121547190.54642529831-0.105620876831-0.80239588230.07333596084830.343323806619-0.01133312917680.792199441909-0.0293262043016-0.04780318894061.392191533790.001653728609060.60681753028637.663636448-19.7575514481-1.89383781728
71.392082580061.50730465965-0.13752403912.160846119280.6016342893335.31666530230.0783280640272-0.47535019774-0.1980177559970.162944095380.3587286424170.210450466661-0.5615704316630.136300698841-0.262700904040.5632551972140.2221360000560.1035316802970.9377715610140.0004802598368630.45278024877429.4369700921-20.446435126-11.9684904532
82.48496900223-2.624721088753.437125444523.27466415847-4.282635244568.482925132550.7426507082790.460554527131-1.2306537593-1.2410352826-0.4516185875890.1635408555832.571667636780.8690845705180.08129875678110.7714748001940.0691369978819-0.005879096813350.6645895818640.03872301949610.71772205782427.6480161879-30.0075037551-12.3839492365
91.759003033440.886900123338-1.417028040141.79167977241-1.197970948744.28986325691-0.0217042390507-0.130606760178-0.02368661115510.1891537774580.0785817580278-0.0601634777211-0.5094219957620.501362082787-0.08195490415830.3869810828540.1209402858040.01324794254780.53829631265-0.1012272449910.3898819481336.0382774137-13.8030349399-33.5624078704
101.962818374161.10656396453-1.255814340123.25024761825-0.4732042105796.748323237090.0696704358635-0.3478620191120.06689263922630.2561802417970.1142675618340.0448695396378-0.2285125143720.496444210633-0.1645214759050.3408143773070.114808776419-0.01548658359740.496217924603-0.05603672841890.36303749978634.8236354905-12.9482471048-30.0813939241
111.892211737730.740717138173-2.459426614220.502862713076-1.613771263866.348146323970.269004984872-0.6843648110780.1245158014740.207544792540.0019803052517-0.0864215710338-0.781026203011.22719973115-0.292011123940.809668187694-0.05839196775740.0419428141590.986237615372-0.1633015867760.50354216771238.7270028813-8.26190932382-17.0754254919
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11(chain A and resid 2:125)2 - 1251 - 124
22(chain A and resid 126:197)126 - 197125 - 172
33(chain A and resid 198:214)198 - 214173 - 189
44(chain A and resid 215:332)215 - 332190 - 301
55(chain A and resid 333:350)333 - 350302 - 309
66(chain A and resid 351:384)351 - 384310 - 331
77(chain A and resid 385:438)385 - 438332 - 376
88(chain A and resid 439:451)439 - 451377 - 389
99(chain A and resid 452:542)452 - 542390 - 480
1010(chain A and resid 543:613)543 - 613481 - 551
1111(chain A and resid 614:664)614 - 664552 - 594

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