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- PDB-6hfg: Structure of the REC114 PH domain -

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Basic information

Entry
Database: PDB / ID: 6hfg
TitleStructure of the REC114 PH domain
ComponentsMeiotic recombination protein REC114
KeywordsRECOMBINATION / Pleckstrin Homology domain Meiotic recombination
Function / homologyMeiotic recombination protein REC114-like / Meiotic recombination protein REC114-like / meiotic DNA double-strand break formation / oogenesis / chromosome / spermatogenesis / DNA recombination / Meiotic recombination protein REC114
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsJuarez-Martinez, A.B. / de Massy, B. / Kadlec, J.
CitationJournal: Life Sci Alliance / Year: 2018
Title: Mouse REC114 is essential for meiotic DNA double-strand break formation and forms a complex with MEI4.
Authors: Kumar, R. / Oliver, C. / Brun, C. / Juarez-Martinez, A.B. / Tarabay, Y. / Kadlec, J. / de Massy, B.
History
DepositionAug 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
B: Meiotic recombination protein REC114


Theoretical massNumber of molelcules
Total (without water)16,2391
Polymers16,2391
Non-polymers00
Water00
1
B: Meiotic recombination protein REC114

B: Meiotic recombination protein REC114


Theoretical massNumber of molelcules
Total (without water)32,4792
Polymers32,4792
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_554-x,-x+y,-z-1/31
Buried area1490 Å2
ΔGint-7 kcal/mol
Surface area12610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.490, 107.490, 82.790
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Meiotic recombination protein REC114


Mass: 16239.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rec114 / Plasmid: pProEXHTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): GOLG / References: UniProt: Q9CWH4

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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: 4.25 Å3/Da / Density % sol: 71.07 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.25 M ammonium sulphate, 0.1 M MES (pH 6.5), 28% PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.5→93 Å / Num. obs: 10262 / % possible obs: 99.6 % / Observed criterion σ(I): 1.1 / Redundancy: 11.2 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 24.2
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 749 / CC1/2: 0.548 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→46.59 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.902 / SU B: 8.425 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.235 / ESU R Free: 0.225 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2887 536 5.3 %RANDOM
Rwork0.23867 ---
obs0.2414 9618 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 77.071 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å2-0.82 Å20 Å2
2---1.64 Å20 Å2
3---5.33 Å2
Refinement stepCycle: 1 / Resolution: 2.5→46.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms899 0 0 0 899
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.014915
X-RAY DIFFRACTIONr_bond_other_d0.0010.017827
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.6391227
X-RAY DIFFRACTIONr_angle_other_deg0.8131.6291934
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1065111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.37521.73946
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.40115166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.99156
X-RAY DIFFRACTIONr_chiral_restr0.0690.2113
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021009
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02183
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.6017.545453
X-RAY DIFFRACTIONr_mcbond_other5.5747.537452
X-RAY DIFFRACTIONr_mcangle_it8.1611.309561
X-RAY DIFFRACTIONr_mcangle_other8.15511.321562
X-RAY DIFFRACTIONr_scbond_it7.158.255461
X-RAY DIFFRACTIONr_scbond_other7.1028.228459
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.60312.05666
X-RAY DIFFRACTIONr_long_range_B_refined12.83480.627912
X-RAY DIFFRACTIONr_long_range_B_other12.84980.76913
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.503→2.568 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.449 22 -
Rwork0.397 687 -
obs--97.52 %

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