[English] 日本語
Yorodumi
- PDB-5pha: PanDDA analysis group deposition -- Crystal Structure of JMJD2D i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5pha
TitlePanDDA analysis group deposition -- Crystal Structure of JMJD2D in complex with N09398a
ComponentsLysine-specific demethylase 4D
KeywordsOXIDOREDUCTASE / PanDDA / SGC - Diamond I04-1 fragment screening / Jmj domain / epigenetics
Function / homology
Function and homology information


positive regulation of chromatin binding / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / positive regulation of double-strand break repair via nonhomologous end joining / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / cellular response to ionizing radiation / double-strand break repair via homologous recombination / regulation of protein phosphorylation ...positive regulation of chromatin binding / [histone H3]-trimethyl-L-lysine9 demethylase / histone H3K9me2/H3K9me3 demethylase activity / positive regulation of double-strand break repair via nonhomologous end joining / histone H3K9 demethylase activity / histone demethylase activity / pericentric heterochromatin / cellular response to ionizing radiation / double-strand break repair via homologous recombination / regulation of protein phosphorylation / HDMs demethylate histones / chromatin DNA binding / site of double-strand break / regulation of gene expression / blood microparticle / damaged DNA binding / inflammatory response / chromatin remodeling / chromatin / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls ...JmjN domain / jmjN domain / JmjN domain profile. / Small domain found in the jumonji family of transcription factors / Cupin / JmjC domain, hydroxylase / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-methylquinazolin-4(3H)-one / NICKEL (II) ION / N-OXALYLGLYCINE / Lysine-specific demethylase 4D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.45 Å
AuthorsPearce, N.M. / Krojer, T. / Talon, R. / Bradley, A.R. / Fairhead, M. / Sethi, R. / Wright, N. / MacLean, E. / Collins, P. / Brandao-Neto, J. ...Pearce, N.M. / Krojer, T. / Talon, R. / Bradley, A.R. / Fairhead, M. / Sethi, R. / Wright, N. / MacLean, E. / Collins, P. / Brandao-Neto, J. / Douangamath, A. / Renjie, Z. / Dias, A. / Vollmar, M. / Ng, J. / Szykowska, A. / Burgess-Brown, N. / Brennan, P.E. / Cox, O. / Oppermann, U. / Bountra, C. / Arrowsmith, C.H. / Edwards, A. / von Delft, F.
CitationJournal: Nat Commun / Year: 2017
Title: A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density.
Authors: Pearce, N.M. / Krojer, T. / Bradley, A.R. / Collins, P. / Nowak, R.P. / Talon, R. / Marsden, B.D. / Kelm, S. / Shi, J. / Deane, C.M. / von Delft, F.
History
DepositionFeb 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_deposit_group
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _pdbx_deposit_group.group_title / _pdbx_deposit_group.group_type
Revision 1.2Oct 4, 2017Group: Structure summary / Category: pdbx_deposit_group / Item: _pdbx_deposit_group.group_title
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _struct_conn.pdbx_dist_value / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lysine-specific demethylase 4D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,52318
Polymers42,0511
Non-polymers1,47217
Water7,170398
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.183, 71.183, 149.739
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-797-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Lysine-specific demethylase 4D / JmjC domain-containing histone demethylation protein 3D / Jumonji domain-containing protein 2D


Mass: 42050.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM4D, JHDM3D, JMJD2D / Production host: escherichia coli (E. coli) / References: UniProt: Q6B0I6

-
Non-polymers , 7 types, 415 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-MEW / 2-methylquinazolin-4(3H)-one


Mass: 160.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8N2O
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O

-
Details

Nonpolymer details yes CC1Nc2ccccc2C(N=1)=O None 4.07 -4.23 -4.23 CC1Nc2ccccc2C(N=1)=O 4 - High Confidence None 0.62 ... yes CC1Nc2ccccc2C(N=1)=O 4.07 -4.23 -4.23 CC1Nc2ccccc2C(N=1)=O 4 - High Confidence None 0.62 43.599999999999994 2.3306751428144303 0.753 0.17599999999999999 0.5 0.1884938106853025 6.74 -22.17 -22.17 CC1Nc2ccccc2C(N=1)=O 4 - High Confidence None 0.5 46.97 1.2201465760497203 0.749 0.21299999999999999 0.5 0.08437861103383995

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.46 % / Mosaicity: 0.06 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 28% PEG3350 -- 0.1M HEPES pH 7.0 -- 0.25M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.45→29.296 Å / Num. obs: 69033 / % possible obs: 99.9 % / Redundancy: 12.9 % / Biso Wilson estimate: 15.1 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.038 / Rrim(I) all: 0.137 / Net I/σ(I): 12.4 / Num. measured all: 888278 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.45-1.4711.10.6823671433060.90.2120.7153.598.4
7.94-29.310.70.10954945140.9820.0350.11520.498.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHENIX1.9_1682refinement
Aimless0.1.27data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4D6R

4d6r


Resolution: 1.45→29.296 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1676 3372 4.89 %
Rwork0.1287 65563 -
obs0.1306 68935 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.84 Å2 / Biso mean: 21.5037 Å2 / Biso min: 9.88 Å2
Refinement stepCycle: final / Resolution: 1.45→29.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2673 0 88 401 3162
Biso mean--38.7 39.08 -
Num. residues----331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063223
X-RAY DIFFRACTIONf_angle_d1.0494394
X-RAY DIFFRACTIONf_chiral_restr0.046426
X-RAY DIFFRACTIONf_plane_restr0.005583
X-RAY DIFFRACTIONf_dihedral_angle_d12.3491243
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4499-1.47060.20571430.14932607275098
1.4706-1.49250.20981460.141326992845100
1.4925-1.51580.18181470.134926862833100
1.5158-1.54070.17711450.123226872832100
1.5407-1.56720.17381250.112426722797100
1.5672-1.59570.15731340.112627332867100
1.5957-1.62640.17061420.107426942836100
1.6264-1.65960.16481370.113426822819100
1.6596-1.69570.17271530.1127112864100
1.6957-1.73520.14531210.108627182839100
1.7352-1.77850.14431470.106226862833100
1.7785-1.82660.1661430.107327012844100
1.8266-1.88040.14671400.107727132853100
1.8804-1.9410.13751600.106326882848100
1.941-2.01040.15161510.112227102861100
2.0104-2.09090.16611200.115327542874100
2.0909-2.1860.14371190.115327492868100
2.186-2.30120.17431330.124927602893100
2.3012-2.44530.19191420.133427312873100
2.4453-2.6340.17981460.133927682914100
2.634-2.89890.16931490.139527512900100
2.8989-3.31790.18061500.136527972947100
3.3179-4.17820.15081400.130228482988100
4.1782-29.30170.18051390.15530183157100

+
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