[English] 日本語
Yorodumi
- PDB-3apm: Crystal structure of the human SNP PAD4 protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3apm
TitleCrystal structure of the human SNP PAD4 protein
ComponentsProtein-arginine deiminase type-4
KeywordsHYDROLASE / alpha/beta-propeller / immunoglobulin-like / arginine citrullination / protein-arginine deiminase / post-translational modification / Calcium binding / histone binding / benzoyl-L-arginine amide binding / nucleus
Function / homology
Function and homology information


histone H3R2 arginine deiminase activity / histone H3R8 arginine deiminase activity / histone H3R17 arginine deiminase activity / histone arginine deiminase activity / histone H3R26 arginine deiminase activity / protein-arginine deiminase / protein-arginine deiminase activity / stem cell population maintenance / Chromatin modifying enzymes / post-translational protein modification ...histone H3R2 arginine deiminase activity / histone H3R8 arginine deiminase activity / histone H3R17 arginine deiminase activity / histone arginine deiminase activity / histone H3R26 arginine deiminase activity / protein-arginine deiminase / protein-arginine deiminase activity / stem cell population maintenance / Chromatin modifying enzymes / post-translational protein modification / protein modification process / nucleosome assembly / chromatin organization / chromatin remodeling / innate immune response / calcium ion binding / protein-containing complex / nucleoplasm / identical protein binding / 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-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHorikoshi, N. / Tachiwana, H. / Saito, K. / Osakabe, A. / Sato, M. / Yamada, M. / Akashi, S. / Nishimura, Y. / Kagawa, W. / Kurumizaka, H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structural and biochemical analyses of the human PAD4 variant encoded by a functional haplotype gene
Authors: Horikoshi, N. / Tachiwana, H. / Saito, K. / Osakabe, A. / Sato, M. / Yamada, M. / Akashi, S. / Nishimura, Y. / Kagawa, W. / Kurumizaka, H.
History
DepositionOct 19, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Nov 1, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein-arginine deiminase type-4


Theoretical massNumber of molelcules
Total (without water)74,4571
Polymers74,4571
Non-polymers00
Water00
1
A: Protein-arginine deiminase type-4

A: Protein-arginine deiminase type-4


Theoretical massNumber of molelcules
Total (without water)148,9152
Polymers148,9152
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4900 Å2
ΔGint-13 kcal/mol
Surface area49050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.556, 61.239, 113.474
Angle α, β, γ (deg.)90.00, 123.85, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Protein-arginine deiminase type-4 / PAD4 / HL-60 PAD / Peptidylarginine deiminase IV / Protein-arginine deiminase type IV


Mass: 74457.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PADI4, PADI5, PDI5 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UM07, protein-arginine deiminase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: imidazole, lithium sulfate, PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 14, 2010
RadiationMonochromator: Rotated-inclined double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 29118 / Num. obs: 28960 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 64.5 Å2 / Rsym value: 0.065 / Net I/σ(I): 12.9
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
2.5-2.593.8327630.641199.5
2.59-2.693.63.629110.526196.5
2.69-2.823.84.528710.4091100
2.82-2.963.86.928850.2721100
2.96-3.153.810.429160.1731100
3.15-3.393.816.529090.1031100
3.39-3.733.82828790.061100
3.73-4.273.838.129180.051100
4.27-5.383.745.129450.047199.9
5.38-503.749.229630.028198.3

-
Processing

Software
NameVersionClassification
BSSdata collection
PHASERphasing
CNS1.21refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WD8

1wd8


Resolution: 2.5→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.287 1469 5.1 %RANDOM
Rwork0.26 ---
all0.286 28999 --
obs0.261 28927 --
Solvent computationBsol: 44.4812 Å2
Displacement parametersBiso mean: 66.6636 Å2
Baniso -1Baniso -2Baniso -3
1--10.823 Å20 Å2-5.015 Å2
2--25.585 Å20 Å2
3----14.762 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.82 Å0.69 Å
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4383 0 0 0 4383
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.473
X-RAY DIFFRACTIONc_mcbond_it1.4831.5
X-RAY DIFFRACTIONc_scbond_it1.7972
X-RAY DIFFRACTIONc_mcangle_it2.6242
X-RAY DIFFRACTIONc_scangle_it2.7882.5
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obsTotal num. of bins used
2.5-2.590.4621430.445X-RAY DIFFRACTION268610
2.59-2.690.4491390.387X-RAY DIFFRACTION275410
2.69-2.820.4131370.363X-RAY DIFFRACTION273510
2.82-2.960.3931350.341X-RAY DIFFRACTION274010
2.96-3.150.4061550.32X-RAY DIFFRACTION274410
3.15-3.390.2931530.288X-RAY DIFFRACTION273610
3.39-3.730.2681420.268X-RAY DIFFRACTION273410
3.73-4.270.281370.224X-RAY DIFFRACTION276610
4.27-5.380.2281670.201X-RAY DIFFRACTION276410
5.38-300.2371610.226X-RAY DIFFRACTION279910
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5cis_peptide.param

+
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