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- PDB-2zjb: Crystal structure of the human Dmc1-M200V polymorphic variant -

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Basic information

Entry
Database: PDB / ID: 2zjb
TitleCrystal structure of the human Dmc1-M200V polymorphic variant
ComponentsMeiotic recombination protein DMC1/LIM15 homologGenetic recombination
KeywordsRECOMBINATION / DNA-BINDING PROTEIN / RING PROTEIN / OCTAMER / AAA ATPASE / ATP-binding / Cell cycle / Meiosis / Nucleotide-binding / Nucleus / Polymorphism
Function / homology
Function and homology information


female gamete generation / chromosome organization involved in meiotic cell cycle / DNA recombinase assembly / homologous chromosome pairing at meiosis / double-strand break repair involved in meiotic recombination / mitotic recombination / DNA strand invasion / DNA strand exchange activity / lateral element / oocyte maturation ...female gamete generation / chromosome organization involved in meiotic cell cycle / DNA recombinase assembly / homologous chromosome pairing at meiosis / double-strand break repair involved in meiotic recombination / mitotic recombination / DNA strand invasion / DNA strand exchange activity / lateral element / oocyte maturation / reciprocal meiotic recombination / ATP-dependent DNA damage sensor activity / male meiosis I / spermatid development / ATP-dependent activity, acting on DNA / ovarian follicle development / meiotic cell cycle / condensed nuclear chromosome / Meiotic recombination / single-stranded DNA binding / site of double-strand break / chromosome / double-stranded DNA binding / spermatogenesis / chromosome, telomeric region / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / nucleus
Similarity search - Function
Meiotic recombination protein Dmc1 / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain ...Meiotic recombination protein Dmc1 / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Meiotic recombination protein DMC1/LIM15 homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsHikiba, J. / Hirota, K. / Kagawa, W. / Ikawa, S. / Kinebuchi, T. / Sakane, I. / Takizawa, Y. / Yokoyama, S. / Mandon-Pepin, B. / Nicolas, A. ...Hikiba, J. / Hirota, K. / Kagawa, W. / Ikawa, S. / Kinebuchi, T. / Sakane, I. / Takizawa, Y. / Yokoyama, S. / Mandon-Pepin, B. / Nicolas, A. / Shibata, T. / Ohta, K. / Kurumizaka, H.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: Structural and functional analyses of the DMC1-M200V polymorphism found in the human population
Authors: Hikiba, J. / Hirota, K. / Kagawa, W. / Ikawa, S. / Kinebuchi, T. / Sakane, I. / Takizawa, Y. / Yokoyama, S. / Mandon-Pepin, B. / Nicolas, A. / Shibata, T. / Ohta, K. / Kurumizaka, H.
History
DepositionMar 2, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Meiotic recombination protein DMC1/LIM15 homolog
B: Meiotic recombination protein DMC1/LIM15 homolog


Theoretical massNumber of molelcules
Total (without water)75,9622
Polymers75,9622
Non-polymers00
Water0
1
A: Meiotic recombination protein DMC1/LIM15 homolog
B: Meiotic recombination protein DMC1/LIM15 homolog

A: Meiotic recombination protein DMC1/LIM15 homolog
B: Meiotic recombination protein DMC1/LIM15 homolog

A: Meiotic recombination protein DMC1/LIM15 homolog
B: Meiotic recombination protein DMC1/LIM15 homolog

A: Meiotic recombination protein DMC1/LIM15 homolog
B: Meiotic recombination protein DMC1/LIM15 homolog


Theoretical massNumber of molelcules
Total (without water)303,8508
Polymers303,8508
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area20730 Å2
ΔGint-107.1 kcal/mol
Surface area77530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.089, 124.089, 217.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Meiotic recombination protein DMC1/LIM15 homolog / Genetic recombination


Mass: 37981.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DMC1 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q14565
Sequence detailsTHE RESIDUE AT POSITION 200 IS A VARIANT AS LISTED IN UNP ENTRY, VAR_018960 IN DMC1_HUMAN.

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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: 2.76 Å3/Da / Density % sol: 55.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 0.1M sodium citrate, 50mM MgCl2, 8% PEG 2000 MME, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MAR CCD 225 mm / Detector: CCD / Date: Oct 4, 2007
RadiationMonochromator: SI DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. all: 11303 / Num. obs: 11293 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.1 % / Rsym value: 0.085 / Net I/σ(I): 33.1
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 6 / Num. unique all: 1096 / Rsym value: 0.464 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V5W

1v5w


Resolution: 3.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.351 1138 RANDOM
Rwork0.294 --
all-11035 -
obs-11034 -
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.71 Å
Luzzati d res low-5 Å
Luzzati sigma a1.26 Å1.38 Å
Refinement stepCycle: LAST / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3748 0 0 0 3748
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.32
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used
3.5-3.620.5911040.537958X-RAY DIFFRACTION10
3.62-3.770.5111050.502984X-RAY DIFFRACTION10
3.77-3.940.431250.368952X-RAY DIFFRACTION10
3.94-4.140.341220.296972X-RAY DIFFRACTION10
4.14-4.40.3291150.284979X-RAY DIFFRACTION10
4.4-4.740.2871210.227961X-RAY DIFFRACTION10
4.74-5.210.2661150.21996X-RAY DIFFRACTION10
5.21-5.940.3341060.225999X-RAY DIFFRACTION10
5.94-7.420.341000.2551030X-RAY DIFFRACTION10
7.42-200.311250.2721065X-RAY DIFFRACTION10

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