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- PDB-6oea: Crystal structure of HMCES SRAP domain in complex with longer 3' ... -

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Basic information

Entry
Database: PDB / ID: 6oea
TitleCrystal structure of HMCES SRAP domain in complex with longer 3' overhang DNA
Components
  • DNA (5'-D(*CP*CP*AP*GP*AP*CP*GP*TP*TP*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 / DNA-binding / Structural Genomics / Structural Genomics Consortium / SGC / HMCES / Protein-DNA 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 / 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
DNA / DNA (> 10) / Abasic site processing protein HMCES
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / 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: 6NLC
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*TP*GP*TP*T)-3')
C: DNA (5'-D(*GP*TP*CP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,47619
Polymers37,1653
Non-polymers31016
Water82946
1
A: Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein
B: DNA (5'-D(*CP*CP*AP*GP*AP*CP*GP*TP*TP*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*TP*GP*TP*T)-3')
C: DNA (5'-D(*GP*TP*CP*TP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,03124
Polymers42,6595
Non-polymers37219
Water543
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)55.863, 52.060, 148.309
Angle α, β, γ (deg.)90.000, 93.110, 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


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, Hydrolases; Acting on peptide bonds (peptidases)

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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*TP*GP*TP*T)-3')


Mass: 3653.390 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, 62 molecules

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


Mass: 62.068 Da / Num. of mol.: 5 / 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.: 46 / 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: 3.02 Å3/Da / Density % sol: 59.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% PEG3350, 0.1 M potassium chloride, 0.1 M Bis-Tris, 0.05 M magnesium chloride

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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→49.11 Å / Num. obs: 25066 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.027 / Rrim(I) all: 0.069 / Net I/σ(I): 15 / Num. measured all: 165977 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.1-2.166.60.8121361120670.9260.3410.8822.299.9
8.91-49.116.10.03321863600.9980.0140.03645.798.9

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Processing

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

5ko9


Resolution: 2.1→49.16 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.2398 / WRfactor Rwork: 0.2016 / FOM work R set: 0.7085 / SU B: 7.002 / SU ML: 0.165 / SU R Cruickshank DPI: 0.1864 / SU Rfree: 0.1662 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1249 5 %RANDOM
Rwork0.2081 ---
obs0.2098 23814 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 178.36 Å2 / Biso mean: 55.262 Å2 / Biso min: 34.72 Å2
Baniso -1Baniso -2Baniso -3
1-3.94 Å20 Å2-1.41 Å2
2--3.78 Å2-0 Å2
3----7.52 Å2
Refinement stepCycle: final / Resolution: 2.1→49.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2050 324 31 46 2451
Biso mean--63.47 54.78 -
Num. residues----274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122490
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182074
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.5743442
X-RAY DIFFRACTIONr_angle_other_deg1.3031.7044821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.85257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.91221.261119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97715334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4681518
X-RAY DIFFRACTIONr_chiral_restr0.0670.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022574
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02550
LS refinement shellResolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 84 -
Rwork0.392 1782 -
all-1866 -
obs--99.84 %

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