[English] 日本語
Yorodumi
- PDB-6ce1: Crystal structure of Peptidyl Arginine Deiminase Type III (PADI3) -

+
Open data


ID or keywords:

Loading...

-
Basic information

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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more