[English] 日本語
Yorodumi
- PDB-7dan: Structure of the Ca2+-bound wild-type peptidylarginine deiminase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dan
TitleStructure of the Ca2+-bound wild-type peptidylarginine deiminase type III (PAD3)
ComponentsProtein-arginine deiminase type-3
KeywordsHYDROLASE / peptidylarginie deiminase / citrullination / post-translational modification / enzyme / active form / calcium / isozyme
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 / 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 / Cupredoxin
Similarity search - Domain/homology
Protein-arginine deiminase type-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSawata, M. / Unno, M.
Funding support Japan, 3items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP25121704 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP23121504 Japan
Japan Society for the Promotion of Science (JSPS)JP19K06507 Japan
CitationJournal: Arch.Biochem.Biophys. / Year: 2021
Title: Structures of human peptidylarginine deiminase type III provide insights into substrate recognition and inhibitor design.
Authors: Funabashi, K. / Sawata, M. / Nagai, A. / Akimoto, M. / Mashimo, R. / Takahara, H. / Kizawa, K. / Thompson, P.R. / Ite, K. / Kitanishi, K. / Unno, M.
History
DepositionOct 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Nov 29, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Protein-arginine deiminase type-3
B: Protein-arginine deiminase type-3
A: Protein-arginine deiminase type-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,40341
Polymers224,4873
Non-polymers1,91638
Water1,06359
1
C: Protein-arginine deiminase type-3
hetero molecules

C: Protein-arginine deiminase type-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,81724
Polymers149,6582
Non-polymers1,15922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6330 Å2
ΔGint-117 kcal/mol
Surface area51990 Å2
MethodPISA
2
B: Protein-arginine deiminase type-3
A: Protein-arginine deiminase type-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,99529
Polymers149,6582
Non-polymers1,33727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7390 Å2
ΔGint-159 kcal/mol
Surface area51840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.648, 115.844, 128.581
Angle α, β, γ (deg.)90.000, 121.340, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 34 or (resid 35...
21(chain B and (resid 1 through 55 or resid 57...
31(chain C and (resid 1 through 34 or (resid 35...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETPROPRO(chain A and (resid 1 through 34 or (resid 35...AC1 - 341 - 34
12GLUGLUGLUGLU(chain A and (resid 1 through 34 or (resid 35...AC3535
13METMETPROPRO(chain A and (resid 1 through 34 or (resid 35...AC1 - 6641 - 664
14METMETPROPRO(chain A and (resid 1 through 34 or (resid 35...AC1 - 6641 - 664
15METMETPROPRO(chain A and (resid 1 through 34 or (resid 35...AC1 - 6641 - 664
21METMETASNASN(chain B and (resid 1 through 55 or resid 57...BB1 - 551 - 55
22GLUGLUGLUGLU(chain B and (resid 1 through 55 or resid 57...BB57 - 12657 - 126
23METMETPROPRO(chain B and (resid 1 through 55 or resid 57...BB1 - 6641 - 664
24METMETPROPRO(chain B and (resid 1 through 55 or resid 57...BB1 - 6641 - 664
25METMETPROPRO(chain B and (resid 1 through 55 or resid 57...BB1 - 6641 - 664
26METMETPROPRO(chain B and (resid 1 through 55 or resid 57...BB1 - 6641 - 664
27METMETPROPRO(chain B and (resid 1 through 55 or resid 57...BB1 - 6641 - 664
28METMETPROPRO(chain B and (resid 1 through 55 or resid 57...BB1 - 6641 - 664
29METMETPROPRO(chain B and (resid 1 through 55 or resid 57...BB1 - 6641 - 664
31METMETPROPRO(chain C and (resid 1 through 34 or (resid 35...CA1 - 341 - 34
32GLUGLUGLUGLU(chain C and (resid 1 through 34 or (resid 35...CA3535
33METMETPROPRO(chain C and (resid 1 through 34 or (resid 35...CA1 - 6641 - 664
34METMETPROPRO(chain C and (resid 1 through 34 or (resid 35...CA1 - 6641 - 664
35METMETPROPRO(chain C and (resid 1 through 34 or (resid 35...CA1 - 6641 - 664
36METMETPROPRO(chain C and (resid 1 through 34 or (resid 35...CA1 - 6641 - 664

-
Components

-
Protein , 1 types, 3 molecules CBA

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


Mass: 74829.102 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PADI3, PAD3, PDI3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ULW8, protein-arginine deiminase

-
Non-polymers , 5 types, 97 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: HEPES, pH 7.5, PEG 200

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9999873570222 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999873570222 Å / Relative weight: 1
ReflectionResolution: 3.1→49.59 Å / Num. obs: 45490 / % possible obs: 99.5 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.029 / Rrim(I) all: 0.077 / Net I/σ(I): 16.8 / Num. measured all: 319843 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.1-3.217.21.0823246444790.9010.4291.1652.299.5
12.01-49.596.90.0356658190.9990.0120.03352.698.3

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D56

7d56


Resolution: 3.1→29.528 Å / SU ML: 0.58 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 38.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3079 2285 5.05 %
Rwork0.2369 42972 -
obs0.2405 45257 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 297.05 Å2 / Biso mean: 131.9872 Å2 / Biso min: 63.77 Å2
Refinement stepCycle: final / Resolution: 3.1→29.528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14740 0 86 59 14885
Biso mean--120.34 89.37 -
Num. residues----1906
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5517X-RAY DIFFRACTION7.323TORSIONAL
12B5517X-RAY DIFFRACTION7.323TORSIONAL
13C5517X-RAY DIFFRACTION7.323TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1001-3.16740.45311570.3427261299
3.1674-3.2410.42661410.3293267699
3.241-3.3220.3851410.3158269499
3.322-3.41170.34931430.2914269199
3.4117-3.51190.38221420.2792267399
3.5119-3.6250.40651350.2838261098
3.625-3.75440.33431430.2497270499
3.7544-3.90440.30621410.2597267299
3.9044-4.08160.39181410.2692268499
4.0816-4.29620.34621420.2426269499
4.2962-4.56450.3061430.2122696100
4.5645-4.91540.28061410.2131268599
4.9154-5.40730.3151420.21265798
5.4073-6.18350.30221450.22322737100
6.1835-7.76710.28621430.24562743100
7.7671-29.5280.23781450.2062274498
Refinement TLS params.Method: refined / Origin x: 44.0052 Å / Origin y: -30.5156 Å / Origin z: 55.2619 Å
111213212223313233
T0.8082 Å2-0.0134 Å20.01 Å2-1.0651 Å20.076 Å2--0.7 Å2
L0.3019 °20.0917 °20.0592 °2-0.241 °20.0387 °2--1.8827 °2
S0.0542 Å °0.0176 Å °0.0149 Å °-0.0118 Å °0.071 Å °0.1181 Å °-0.0407 Å °-0.723 Å °-0.117 Å °
Refinement TLS groupSelection details: all

+
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://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