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- PDB-6oov: Crystal structure of HMCES SRAP domain in complex with palindromi... -

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Basic information

Entry
Database: PDB / ID: 6oov
TitleCrystal structure of HMCES SRAP domain in complex with palindromic 3' overhang DNA
Components
  • DNA (5'-D(*CP*AP*AP*CP*GP*TP*TP*GP*TP*TP*TP*TP*T)-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


: / positive regulation of isotype switching / double-strand break repair via alternative nonhomologous end joining / Hydrolases; Acting on peptide bonds (peptidases) / replication fork / single-stranded DNA binding / peptidase activity / 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: 2.2 Å
AuthorsHalabelian, L. / Zeng, H. / Li, Y. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of HMCES SRAP domain in complex with palindromic 3' overhang DNA
Authors: Halabelian, L. / Zeng, H. / Li, Y. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Structural Genomics Consortium (SGC)
History
DepositionApr 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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: Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein
C: DNA (5'-D(*CP*AP*AP*CP*GP*TP*TP*GP*TP*TP*TP*TP*T)-3')
D: DNA (5'-D(*CP*AP*AP*CP*GP*TP*TP*GP*TP*TP*TP*TP*T)-3')


Theoretical massNumber of molelcules
Total (without water)71,23851
Polymers71,2384
Non-polymers047
Water1,47782
1
A: Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein
C: DNA (5'-D(*CP*AP*AP*CP*GP*TP*TP*GP*TP*TP*TP*TP*T)-3')
D: DNA (5'-D(*CP*AP*AP*CP*GP*TP*TP*GP*TP*TP*TP*TP*T)-3')

B: Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein


Theoretical massNumber of molelcules
Total (without water)71,23851
Polymers71,2384
Non-polymers047
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
Buried area4100 Å2
ΔGint-21 kcal/mol
Surface area25360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.729, 139.828, 66.613
Angle α, β, γ (deg.)90.000, 99.990, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 0 / Auth seq-ID: 2 - 270 / Label seq-ID: 1 - 269

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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: 31671.617 Da / Num. of mol.: 2
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: DNA chain DNA (5'-D(*CP*AP*AP*CP*GP*TP*TP*GP*TP*TP*TP*TP*T)-3')


Mass: 3947.581 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 47 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.94 Å3/Da / Density % sol: 58.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 11% PEG 8K, 0.1M CaCl2, 0.1M 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.2→47.84 Å / Num. obs: 41672 / % possible obs: 99.7 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.035 / Rrim(I) all: 0.066 / Net I/σ(I): 13.8 / Num. measured all: 142073 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.3 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.270.6461199936100.810.4160.7711.799.9
9.07-47.840.01820496190.9990.0120.02248.599.3

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6OEB

6oeb


Resolution: 2.2→47.84 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 14.2 / SU ML: 0.162 / SU R Cruickshank DPI: 0.1992 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.166
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2192 2059 4.9 %RANDOM
Rwork0.1936 ---
obs0.1948 39582 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 156.62 Å2 / Biso mean: 55.49 Å2 / Biso min: 15.57 Å2
Baniso -1Baniso -2Baniso -3
1--2.25 Å20 Å21.79 Å2
2---2.67 Å2-0 Å2
3---4.04 Å2
Refinement stepCycle: final / Resolution: 2.2→47.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3940 462 47 82 4531
Biso mean--46.98 52.21 -
Num. residues----524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0124566
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183824
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.596311
X-RAY DIFFRACTIONr_angle_other_deg1.2991.6758884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3015495
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.30121.273220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.94115620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2181532
X-RAY DIFFRACTIONr_chiral_restr0.0660.2588
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024827
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02997
Refine LS restraints NCS

Ens-ID: 1 / Number: 7881 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 173 -
Rwork0.313 2918 -
all-3091 -
obs--99.84 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.03110.27960.15822.16630.2631.94490.0848-0.0939-0.38290.1422-0.063-0.08020.1134-0.0136-0.02180.0391-0.00920.06920.00470.00250.336810.2606-3.876717.5301
23.81890.24530.02233.24190.03321.7250.0154-0.42990.04030.4264-0.01280.00920.0175-0.0198-0.00260.0797-0.00250.06540.0558-0.02250.1953-6.485624.359428.2117
33.9752-0.7077-0.52281.94042.43729.16640.02540.2153-0.0903-0.2978-0.40530.1567-0.251-1.46840.37990.2683-0.0176-0.0010.2567-0.09760.4583-2.7537-17.1586-3.7643
40.99030.8848-0.30056.59054.85415.8992-0.053-0.16430.31760.1075-0.19690.5219-0.03580.0250.24990.21830.0953-0.00530.179-0.01280.3853-3.5066-22.948-16.2215
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 270
2X-RAY DIFFRACTION2B2 - 270
3X-RAY DIFFRACTION3C0 - 10
4X-RAY DIFFRACTION4D-1 - 10

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