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- PDB-5ko9: Crystal Structure of the SRAP Domain of Human HMCES Protein -

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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 / protein-DNA covalent cross-linking repair / Hydrolases; Acting on peptide bonds (peptidases) / double-strand break repair via alternative nonhomologous end joining / somatic hypermutation of immunoglobulin genes / interstrand cross-link repair / replication fork ...protein-DNA covalent cross-linking activity / Lyases / DNA-(abasic site) binding / positive regulation of isotype switching / protein-DNA covalent cross-linking repair / Hydrolases; Acting on peptide bonds (peptidases) / double-strand break repair via alternative nonhomologous end joining / somatic hypermutation of immunoglobulin genes / interstrand cross-link repair / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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 %

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