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- PDB-4y66: Crystal structure of Giardia lamblia Hop2-Mnd1 complex -

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Basic information

Entry
Database: PDB / ID: 4y66
TitleCrystal structure of Giardia lamblia Hop2-Mnd1 complex
Components
  • Mnd1
  • Putative tbpip family protein
KeywordsCELL CYCLE
Function / homology
Function and homology information


reciprocal meiotic recombination / double-stranded DNA binding / nucleus
Similarity search - Function
Meiotic nuclear division protein 1 / Mnd1, HTH domain / Mnd1 HTH domain / Homologous-pairing protein 2, winged helix domain / Homologous-pairing protein 2 / Leucine zipper with capping helix domain / TBPIP/Hop2 winged helix domain / Leucine zipper with capping helix domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Mnd1 / Putative tbpip family protein
Similarity search - Component
Biological speciesGiardia lamblia ATCC 50803 (eukaryote)
Giardia lamblia (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsKang, H.A. / Shin, H.C. / Oh, B.H.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Crystal structure of Hop2-Mnd1 and mechanistic insights into its role in meiotic recombination
Authors: Kang, H.A. / Shin, H.C. / Kalantzi, A.S. / Toseland, C.P. / Kim, H.M. / Gruber, S. / Peraro, M.D. / Oh, B.H.
History
DepositionFeb 12, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mnd1
B: Putative tbpip family protein
C: Mnd1
D: Putative tbpip family protein
E: Mnd1
F: Putative tbpip family protein


Theoretical massNumber of molelcules
Total (without water)147,1546
Polymers147,1546
Non-polymers00
Water0
1
A: Mnd1
B: Putative tbpip family protein


Theoretical massNumber of molelcules
Total (without water)49,0512
Polymers49,0512
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-61 kcal/mol
Surface area16930 Å2
MethodPISA
2
C: Mnd1
D: Putative tbpip family protein


Theoretical massNumber of molelcules
Total (without water)49,0512
Polymers49,0512
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7540 Å2
ΔGint-72 kcal/mol
Surface area24410 Å2
MethodPISA
3
E: Mnd1
F: Putative tbpip family protein


Theoretical massNumber of molelcules
Total (without water)49,0512
Polymers49,0512
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-46 kcal/mol
Surface area19370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.847, 69.066, 292.137
Angle α, β, γ (deg.)90.00, 95.34, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Mnd1


Mass: 23311.662 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Giardia lamblia ATCC 50803 (eukaryote) / Strain: ATCC 50803 / Gene: GL50803_6626 / Production host: Escherichia coli (E. coli) / References: UniProt: E2RTU1
#2: Protein Putative tbpip family protein / Hop2


Mass: 25739.529 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Giardia lamblia (eukaryote) / Strain: ATCC 50803 / Gene: GSB_17044 / Production host: Escherichia coli (E. coli) / References: UniProt: V6TR15

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 69.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Tascimate, Tris

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97889 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 10, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97889 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 34750 / % possible obs: 87 % / Redundancy: 3.8 % / Net I/σ(I): 22.1
Reflection shellHighest resolution: 3.2 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.272 / % possible all: 64.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→40.65 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.78 / Phase error: 29.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.286 1704 4.98 %
Rwork0.239 --
obs0.241 34247 87.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→40.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7214 0 0 0 7214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117281
X-RAY DIFFRACTIONf_angle_d1.349909
X-RAY DIFFRACTIONf_dihedral_angle_d17.2472546
X-RAY DIFFRACTIONf_chiral_restr0.0511238
X-RAY DIFFRACTIONf_plane_restr0.0071292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.29420.42481100.35162052X-RAY DIFFRACTION66
3.2942-3.40040.31581200.32362271X-RAY DIFFRACTION74
3.4004-3.52190.32161150.29282328X-RAY DIFFRACTION77
3.5219-3.66280.31081360.26762548X-RAY DIFFRACTION83
3.6628-3.82940.30151440.24842670X-RAY DIFFRACTION86
3.8294-4.03120.26031410.22632784X-RAY DIFFRACTION90
4.0312-4.28350.23461600.21352838X-RAY DIFFRACTION92
4.2835-4.61380.22251460.20762926X-RAY DIFFRACTION95
4.6138-5.07730.27171530.21222936X-RAY DIFFRACTION96
5.0773-5.81020.30071600.24572999X-RAY DIFFRACTION96
5.8102-7.31320.31161590.27793020X-RAY DIFFRACTION96
7.3132-40.65730.28541600.20563171X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 20.6299 Å / Origin y: 56.7855 Å / Origin z: -50.0752 Å
111213212223313233
T0.175 Å2-0.0645 Å2-0.0329 Å2-0.1731 Å20.2472 Å2--0.1417 Å2
L-0.0927 °20.0663 °2-0.132 °2-0.0442 °20.0213 °2--0.0397 °2
S-0.1132 Å °0.0019 Å °0.0242 Å °-0.1263 Å °-0.1175 Å °-0.0022 Å °-0.0359 Å °0.0765 Å °-0.0956 Å °
Refinement TLS groupSelection details: ALL

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