[English] 日本語
Yorodumi
- PDB-5xsl: Crystal structure of the PWWP domain of human hepatoma-derived gr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xsl
TitleCrystal structure of the PWWP domain of human hepatoma-derived growth factor
ComponentsHepatoma-derived growth factor
KeywordsHORMONE / Growth factor
Function / homology
Function and homology information


cellular response to interleukin-7 / positive regulation of cell division / protein localization to nucleus / transcription repressor complex / tubulin binding / transcription corepressor binding / growth factor activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription corepressor activity / heparin binding ...cellular response to interleukin-7 / positive regulation of cell division / protein localization to nucleus / transcription repressor complex / tubulin binding / transcription corepressor binding / growth factor activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / transcription corepressor activity / heparin binding / negative regulation of neuron apoptotic process / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / nucleotide binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular space / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain
Similarity search - Domain/homology
Hepatoma-derived growth factor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsChen, L.Y. / Huang, Y.C. / Hsieh, Y.C. / Lin, P.J. / Chen, C.J.
CitationJournal: To Be Published
Title: Structure of the PWWP domain at 3.3 Angstroms resolution
Authors: Chen, L.Y. / Huang, Y.C. / Hsieh, Y.C. / Lin, P.J.
History
DepositionJun 14, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hepatoma-derived growth factor


Theoretical massNumber of molelcules
Total (without water)13,7351
Polymers13,7351
Non-polymers00
Water543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5650 Å2
Unit cell
Length a, b, c (Å)79.490, 79.490, 105.099
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

-
Components

#1: Protein Hepatoma-derived growth factor / HDGF


Mass: 13735.487 Da / Num. of mol.: 1 / Fragment: UNP residues 1-100
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Hdgf / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): Codon plus-RIL / References: UniProt: Q8VHK7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.49 Å3/Da / Density % sol: 64.75 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / Details: ammonium sulfate, Tris, PEG 3350

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Dec 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. obs: 3320 / % possible obs: 100 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.081 / Rsym value: 0.141 / Net I/σ(I): 21.89
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 3.59 / CC1/2: 0.958 / Rsym value: 0.705 / Χ2: 0.94 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QBY

3qby


Resolution: 3.3→30 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.83 / SU B: 23.06 / SU ML: 0.384 / Cross valid method: THROUGHOUT / ESU R: 2.161 / ESU R Free: 0.477 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28218 166 5.4 %RANDOM
Rwork0.22542 ---
obs0.22854 2898 93.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 73.808 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20.48 Å20 Å2
2--0.95 Å2-0 Å2
3----3.09 Å2
Refinement stepCycle: 1 / Resolution: 3.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms699 0 0 3 702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.019722
X-RAY DIFFRACTIONr_bond_other_d0.0030.02661
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.952970
X-RAY DIFFRACTIONr_angle_other_deg1.04731540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.846583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.48124.44436
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.83515124
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.272152
X-RAY DIFFRACTIONr_chiral_restr0.1020.291
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021800
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02170
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.077.145338
X-RAY DIFFRACTIONr_mcbond_other5.0627.15337
X-RAY DIFFRACTIONr_mcangle_it8.210.659419
X-RAY DIFFRACTIONr_mcangle_other8.19110.652420
X-RAY DIFFRACTIONr_scbond_it4.9327.451384
X-RAY DIFFRACTIONr_scbond_other4.9267.447385
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.10610.948552
X-RAY DIFFRACTIONr_long_range_B_refined11.79955.29835
X-RAY DIFFRACTIONr_long_range_B_other11.79455.288836
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.296→3.382 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.192 5 -
Rwork0.236 127 -
obs--58.67 %

+
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