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- PDB-6oeb: Crystal structure of HMCES SRAP domain in complex with 3' overhang DNA -

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Basic information

Entry
Database: PDB / ID: 6oeb
TitleCrystal structure of HMCES SRAP domain in complex with 3' overhang DNA
Components
  • DNA (5'-D(*CP*CP*AP*GP*AP*CP*GP*TP*T)-3')
  • DNA (5'-D(*GP*TP*CP*TP*GP*G)-3')
  • Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein
KeywordsDNA BINDING PROTEIN/DNA / SRAP Domain / HMCES / Structural Genomics / Structural Genomics Consortium / SGC / DNA binding protein / DNA-protein complex / DNA-damage protein / 3' overhang / DNA BINDING PROTEIN-DNA complex
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
DNA / Abasic site processing protein HMCES
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHalabelian, L. / Ravichandran, M. / Li, Y. / Zeng, H. / 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
DepositionMar 27, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionApr 10, 2019ID: 6NLD
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author
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 / _citation_author.name
Revision 1.2Jul 10, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jul 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein
B: DNA (5'-D(*CP*CP*AP*GP*AP*CP*GP*TP*T)-3')
C: DNA (5'-D(*GP*TP*CP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,60020
Polymers36,2283
Non-polymers37217
Water1,38777
1
A: Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein
B: DNA (5'-D(*CP*CP*AP*GP*AP*CP*GP*TP*T)-3')
C: DNA (5'-D(*GP*TP*CP*TP*GP*G)-3')
hetero molecules

B: DNA (5'-D(*CP*CP*AP*GP*AP*CP*GP*TP*T)-3')
C: DNA (5'-D(*GP*TP*CP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,21824
Polymers40,7845
Non-polymers43419
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_444-x-1/2,y-1/2,-z-1/21
Unit cell
Length a, b, c (Å)55.728, 51.151, 149.210
Angle α, β, γ (deg.)90.000, 92.770, 90.000
Int Tables number5
Space group name H-MI121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 31671.617 Da / Num. of mol.: 1 / Fragment: SRAP domain (UNP residues 2-270)
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

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(*CP*CP*AP*GP*AP*CP*GP*TP*T)-3')


Mass: 2715.799 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*TP*CP*TP*GP*G)-3')


Mass: 1840.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 94 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 11 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 3 Å3/Da / Density % sol: 59.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 25% PEG3350, 0.2 M ammonium sulfate, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 18, 2018
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.1→48.38 Å / Num. obs: 24718 / % possible obs: 99.8 % / Redundancy: 4.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.042 / Rrim(I) all: 0.09 / Net I/σ(I): 10.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.1-2.164.30.8620210.8140.4620.9899.7
8.91-48.3840.0373540.9930.0220.04499.2

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5KO9

5ko9


Resolution: 2.1→48.38 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 7.839 / SU ML: 0.177 / SU R Cruickshank DPI: 0.1889 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.164
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2359 1232 5 %RANDOM
Rwork0.2058 ---
obs0.2074 23486 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 126.72 Å2 / Biso mean: 46.772 Å2 / Biso min: 29.86 Å2
Baniso -1Baniso -2Baniso -3
1-2.51 Å20 Å2-0.9 Å2
2--3.58 Å2-0 Å2
3----5.98 Å2
Refinement stepCycle: final / Resolution: 2.1→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2063 302 35 77 2477
Biso mean--57.52 47.49 -
Num. residues----272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122493
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182088
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.5813439
X-RAY DIFFRACTIONr_angle_other_deg1.3061.6954856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8835258
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.15421.21124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10715342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0561519
X-RAY DIFFRACTIONr_chiral_restr0.0640.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022590
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02557
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 77 -
Rwork0.363 1743 -
all-1820 -
obs--99.73 %

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