[English] 日本語
Yorodumi
- PDB-4n2b: Crystal structure of Protein Arginine Deiminase 2 (10 mM Ca2+) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4n2b
TitleCrystal structure of Protein Arginine Deiminase 2 (10 mM Ca2+)
ComponentsProtein-arginine deiminase type-2
KeywordsHYDROLASE / deiminase
Function / homology
Function and homology information


negative regulation of lymphocyte chemotaxis / histone arginine deiminase activity / histone H3R26 arginine deiminase activity / protein-arginine deiminase / negative regulation of chemokine-mediated signaling pathway / protein-arginine deiminase activity / Chromatin modifying enzymes / estrogen receptor signaling pathway / substantia nigra development / transcription initiation-coupled chromatin remodeling ...negative regulation of lymphocyte chemotaxis / histone arginine deiminase activity / histone H3R26 arginine deiminase activity / protein-arginine deiminase / negative regulation of chemokine-mediated signaling pathway / protein-arginine deiminase activity / Chromatin modifying enzymes / estrogen receptor signaling pathway / substantia nigra development / transcription initiation-coupled chromatin remodeling / cellular response to leukemia inhibitory factor / nuclear estrogen receptor binding / euchromatin / azurophil granule lumen / chromatin remodeling / calcium ion binding / Neutrophil degranulation / protein homodimerization activity / extracellular exosome / extracellular region / nucleus / cytosol / cytoplasm
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-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsSlade, D.J. / Zhang, X. / Fang, P. / Dreyton, C.J. / Zhang, Y. / Gross, M.L. / Guo, M. / Coonrod, S.A. / Thompson, P.R.
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: Protein arginine deiminase 2 binds calcium in an ordered fashion: implications for inhibitor design.
Authors: Slade, D.J. / Fang, P. / Dreyton, C.J. / Zhang, Y. / Fuhrmann, J. / Rempel, D. / Bax, B.D. / Coonrod, S.A. / Lewis, H.D. / Guo, M. / Gross, M.L. / Thompson, P.R.
History
DepositionOct 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: 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 / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein-arginine deiminase type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,34610
Polymers78,6731
Non-polymers6739
Water13,727762
1
A: Protein-arginine deiminase type-2
hetero molecules

A: Protein-arginine deiminase type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,69220
Polymers157,3462
Non-polymers1,34618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8520 Å2
ΔGint-212 kcal/mol
Surface area52850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.665, 51.549, 76.217
Angle α, β, γ (deg.)90.000, 105.760, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1375-

HOH

-
Components

#1: Protein Protein-arginine deiminase type-2 / PAD-H19 / Peptidylarginine deiminase II / Protein-arginine deiminase type II


Mass: 78673.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PADI2, KIAA0994, PDI2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y2J8, protein-arginine deiminase
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 762 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 5.6
Details: 10-20% MPD, 50 mM MES, pH 5.6, 0.12 M sodium acetate, VAPOR DIFFUSION, SITTING DROP

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 1, 2003 / Details: beryllium lenses
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.69→40.393 Å / Num. obs: 79078 / % possible obs: 99.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 14.01 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 17.6
Reflection shellHighest resolution: 1.69 Å / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 2.4

-
Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4N25

4n25


Resolution: 1.69→40.393 Å / Occupancy max: 1 / Occupancy min: 0.22 / FOM work R set: 0.8742 / SU ML: 0.41 / σ(F): 1.36 / Phase error: 19.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2002 2000 2.53 %
Rwork0.1675 --
obs0.1683 79077 92.8 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.039 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso max: 82.1 Å2 / Biso mean: 20.0622 Å2 / Biso min: 4.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.1814 Å20 Å2-0.292 Å2
2--1.2075 Å20 Å2
3----0.0261 Å2
Refinement stepCycle: LAST / Resolution: 1.69→40.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5152 0 37 762 5951
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115413
X-RAY DIFFRACTIONf_angle_d1.3377416
X-RAY DIFFRACTIONf_chiral_restr0.114813
X-RAY DIFFRACTIONf_plane_restr0.009938
X-RAY DIFFRACTIONf_dihedral_angle_d14.6871987
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.69-1.75010.23211110.21794298440952
1.7501-1.82020.26221700.20226515668579
1.8202-1.9030.2362070.19157997820496
1.903-2.00330.21732140.179582598473100
2.0033-2.12880.19942140.171782578471100
2.1288-2.29320.20272150.172182678482100
2.2932-2.52390.21292150.168682808495100
2.5239-2.8890.20412160.169783278543100
2.889-3.63950.18422170.161683678584100
3.6395-40.40430.17762210.14885108731100
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)
12.1196-1.12851.10231.3895-0.27173.29410.11820.15570.1334-0.1333-0.1010.127-0.24160.0357-0.0070.11820.0281-0.01960.0558-0.0460.1416-43.419913.8231-3.4688
22.6108-2.0860.36933.3721-0.56950.41910.240.195-0.2242-0.2484-0.08240.1978-0.0163-0.037-0.11070.15610.1511-0.13010.0546-0.08610.2646-55.429812.4142-9.0378
32.9133-0.30290.94280.2090.07460.5467-0.109-0.36170.29920.0401-0.0279-0.05820.0097-0.05880.06950.06750.00760.01260.11450.01320.0637-13.19044.407517.0977
42.5503-1.08950.51821.3987-0.37611.3658-0.0384-0.4488-0.20260.12080.00770.01840.0436-0.02610.00710.0538-0.02690.02890.2340.02540.054-17.8601-4.61423.2212
50.16290.18520.01420.5901-0.53220.76710.03-0.3401-0.19920.0592-0.01590.06670.0646-0.02910.02130.0832-0.01820.00870.14950.02080.074-23.7851-8.198217.5719
61.5853-0.18840.87750.30550.00020.783-0.0068-0.0868-0.14740.00160.03120.00250.0714-0.0301-0.02220.052-0.00120.02260.07030.01640.0512-8.7921-3.365516.1191
76.9268-0.1420.54985.7649-1.20282.1502-0.0886-0.4190.11280.28510.09750.0309-0.4003-0.2093-0.0070.26150.10210.0070.1876-0.02620.037820.3219-4.046739.4876
81.9994-0.906-0.00182.7522-0.03162.0675-0.0579-0.305-0.11690.14030.0063-0.0880.1545-0.06770.03440.0599-0.00730.00020.12790.05380.04157.5105-4.83824.5481
98.74821.34812.05732.289-3.32536.8582-0.2987-0.0137-0.94960.3357-0.02460.12731.28490.08330.3020.2625-0.034-0.00690.11540.04550.26211.09-15.806418.8723
102.31662.09461.8872.05032.0652.3602-0.3316-1.512-1.5241.1370.72080.31390.87860.2477-0.3840.54230.1573-0.14390.59520.17310.62719.3469-16.414928.3341
115.6472-1.5202-3.61323.27761.17434.0725-0.16560.1801-0.6444-0.07920.0287-0.06790.4673-0.39150.20960.1136-0.0493-0.02830.17050.09690.13615.3524-14.13720.2252
121.5202-0.3452-0.27550.5180.52350.69270.0370.07810.0159-0.0695-0.00540.03410.0043-0.0481-0.02140.07480.00160.00740.02510.02690.069117.5066-3.665111.0717
134.2921-1.13060.62111.0161-0.1241.4609-0.08780.03580.09610.0648-0.002-0.011-0.20460.1280.01550.0898-0.0044-0.00030.0062-0.01260.042738.07373.866322.7794
146.15335.9533-5.50367.1135-6.56776.0865-0.1101-0.01-0.3852-0.06590.0512-0.46390.36150.10510.05730.12230.0349-0.05010.1126-0.01340.121846.1952-12.422830.1228
151.14920.07090.21260.4492-0.18651.3478-0.040.0772-0.04050.00070.0568-0.02950.02940.1564-0.01140.05950.00080.00550.0214-0.02540.05934.2513-2.315217.6501
161.4848-0.3691-0.08523.7638-0.64571.2882-0.0097-0.1682-0.0639-0.04090.07320.095-0.03860.0286-0.05750.09250.0062-0.00740.0593-0.01470.024835.5385-0.867332.4095
173.4656-1.51252.5672.5583-2.23382.9751-0.00240.05960.0739-0.0636-0.044-0.08850.13160.1370.0390.06920.03170.03020.0835-0.02650.08778.93423.285520.1947
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 3:96)A3 - 96
2X-RAY DIFFRACTION2(chain A and resid 97:112)A97 - 112
3X-RAY DIFFRACTION3(chain A and resid 113:163)A113 - 163
4X-RAY DIFFRACTION4(chain A and resid 164:193)A164 - 193
5X-RAY DIFFRACTION5(chain A and resid 194:242)A194 - 242
6X-RAY DIFFRACTION6(chain A and resid 243:318)A243 - 318
7X-RAY DIFFRACTION7(chain A and resid 319:346)A319 - 346
8X-RAY DIFFRACTION8(chain A and resid 347:369)A347 - 369
9X-RAY DIFFRACTION9(chain A and resid 370:373)A370 - 373
10X-RAY DIFFRACTION10(chain A and resid 381:382)A381 - 382
11X-RAY DIFFRACTION11(chain A and resid 383:402)A383 - 402
12X-RAY DIFFRACTION12(chain A and resid 403:475)A403 - 475
13X-RAY DIFFRACTION13(chain A and resid 476:514)A476 - 514
14X-RAY DIFFRACTION14(chain A and resid 515:530)A515 - 530
15X-RAY DIFFRACTION15(chain A and resid 531:607)A531 - 607
16X-RAY DIFFRACTION16(chain A and resid 608:644)A608 - 644
17X-RAY DIFFRACTION17(chain A and resid 645:668)A645 - 668

+
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