[English] 日本語
Yorodumi
- PDB-5ko9: Crystal Structure of the SRAP Domain of Human HMCES Protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ko9
TitleCrystal Structure of the SRAP Domain of Human HMCES Protein
ComponentsEmbryonic stem cell-specific 5-hydroxymethylcytosine-binding protein
KeywordsDNA BINDING PROTEIN / SRAP Domain / DNA-binding / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


protein-DNA covalent cross-linking activity / Lyases / DNA-(abasic site) binding / positive regulation of isotype switching / double-strand break repair via alternative nonhomologous end joining / protein-DNA covalent cross-linking repair / Hydrolases; Acting on peptide bonds (peptidases) / interstrand cross-link repair / somatic hypermutation of immunoglobulin genes / replication fork ...protein-DNA covalent cross-linking activity / Lyases / DNA-(abasic site) binding / positive regulation of isotype switching / double-strand break repair via alternative nonhomologous end joining / protein-DNA covalent cross-linking repair / Hydrolases; Acting on peptide bonds (peptidases) / interstrand cross-link repair / somatic hypermutation of immunoglobulin genes / replication fork / peptidase activity / single-stranded DNA binding / DNA damage response / proteolysis
Similarity search - Function
SOS response associated peptidase-like / hypothetical protein yedk fold / SOS response associated peptidase (SRAP) / SOS response associated peptidase-like / SOS response associated peptidase (SRAP) / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Abasic site processing protein HMCES
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHalabelian, L. / Li, Y. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2019
Title: Structural basis of HMCES interactions with abasic DNA and multivalent substrate recognition.
Authors: Halabelian, L. / Ravichandran, M. / Li, Y. / Zeng, H. / Rao, A. / Aravind, L. / Arrowsmith, C.H.
History
DepositionJun 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Oct 4, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein


Theoretical massNumber of molelcules
Total (without water)31,80345
Polymers31,8031
Non-polymers044
Water3,351186
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.102, 44.745, 82.901
Angle α, β, γ (deg.)90.000, 107.150, 90.000
Int Tables number5
Space group name H-MI121

-
Components

#1: Protein Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein / ES cell-specific 5hmC-binding protein / Putative peptidase SRAPD1 / SRAP domain-containing protein 1


Mass: 31802.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HMCES, C3orf37, DC12, SRAPD1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96FZ2, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 44 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 44.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M BTP, 2% Tacsimate, 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.5→48.37 Å / Num. obs: 43639 / % possible obs: 97 % / Redundancy: 3.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Net I/σ(I): 15.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.5-1.533.40.6791.90.667193.2
8.22-48.373.70.02649.80.999198.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2F20, 2BDV, 2ICU, 1ZN6

2f20

2bdv

2icu

1zn6


Resolution: 1.5→48.37 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.549 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.076
RfactorNum. reflection% reflectionSelection details
Rfree0.2093 2132 4.9 %RANDOM
Rwork0.1818 ---
obs0.1831 41504 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 83.46 Å2 / Biso mean: 24.169 Å2 / Biso min: 12.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.76 Å2-0 Å20.93 Å2
2---0.61 Å2-0 Å2
3---0.67 Å2
Refinement stepCycle: final / Resolution: 1.5→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 44 186 2216
Biso mean--35.67 31.48 -
Num. residues----253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192129
X-RAY DIFFRACTIONr_bond_other_d0.0020.021937
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.9422917
X-RAY DIFFRACTIONr_angle_other_deg0.97134462
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3985275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.35722.843102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.56915340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0391521
X-RAY DIFFRACTIONr_chiral_restr0.0890.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212461
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02520
X-RAY DIFFRACTIONr_mcbond_it1.5742.3681040
X-RAY DIFFRACTIONr_mcbond_other1.5722.3651039
X-RAY DIFFRACTIONr_mcangle_it2.473.5431305
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 151 -
Rwork0.284 2976 -
all-3127 -
obs--93.51 %

+
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