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- PDB-8cxk: Structure of the C. elegans HIM-3 R93Y mutant -

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Basic information

Entry
Database: PDB / ID: 8cxk
TitleStructure of the C. elegans HIM-3 R93Y mutant
ComponentsHORMA domain-containing protein
KeywordsPEPTIDE BINDING PROTEIN / meiotic HORMAD / PCH-2 / HORMA domain / Hop1
Function / homology
Function and homology information


regulation of centriole-centriole cohesion / meiotic chromosome segregation / homologous chromosome segregation / synaptonemal complex assembly / homologous chromosome pairing at meiosis / synaptonemal complex / lateral element / reciprocal meiotic recombination / sister chromatid cohesion / condensed nuclear chromosome ...regulation of centriole-centriole cohesion / meiotic chromosome segregation / homologous chromosome segregation / synaptonemal complex assembly / homologous chromosome pairing at meiosis / synaptonemal complex / lateral element / reciprocal meiotic recombination / sister chromatid cohesion / condensed nuclear chromosome / chromosome / DNA binding
Similarity search - Function
HORMA domain / HORMA domain / HORMA domain profile. / HORMA domain superfamily
Similarity search - Domain/homology
HORMA domain-containing protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsEgo, K.M. / Russo, A. / Giacopazzi, S. / Deshong, A. / Menon, M. / Ortiz, V. / Bhalla, N. / Corbett, K.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM144121 United States
CitationJournal: Plos Genet. / Year: 2023
Title: The conserved AAA ATPase PCH-2 distributes its regulation of meiotic prophase events through multiple meiotic HORMADs in C. elegans.
Authors: Russo, A.E. / Giacopazzi, S. / Deshong, A. / Menon, M. / Ortiz, V. / Ego, K.M. / Corbett, K.D. / Bhalla, N.
History
DepositionMay 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HORMA domain-containing protein


Theoretical massNumber of molelcules
Total (without water)33,1731
Polymers33,1731
Non-polymers00
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.234, 73.234, 110.816
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein HORMA domain-containing protein / Meiotic chromosome core protein


Mass: 33172.809 Da / Num. of mol.: 1 / Mutation: R93Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: him-3, CELE_ZK381.1, ZK381.1 / Production host: Escherichia coli (E. coli) / References: UniProt: G5EBG0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.59 Å3/Da / Density % sol: 52.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.4-1.6 M sodium malonate pH 6.5-7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.3→70 Å / Num. obs: 82280 / % possible obs: 100 % / Redundancy: 19.8 % / Biso Wilson estimate: 19.36 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.056 / Net I/σ(I): 27.38
Reflection shellResolution: 1.3→1.38 Å / Redundancy: 19.7 % / Rmerge(I) obs: 2.027 / Num. unique obs: 13303 / CC1/2: 0.677 / Rrim(I) all: 2.081 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TRK

4trk


Resolution: 1.3→63.42 Å / SU ML: 0.1672 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.794
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1639 4255 5.17 %
Rwork0.1439 78019 -
obs0.1449 82274 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.1 Å2
Refinement stepCycle: LAST / Resolution: 1.3→63.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1929 0 0 252 2181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02131975
X-RAY DIFFRACTIONf_angle_d1.57952658
X-RAY DIFFRACTIONf_chiral_restr0.1078288
X-RAY DIFFRACTIONf_plane_restr0.0144341
X-RAY DIFFRACTIONf_dihedral_angle_d14.9567739
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.320.38671330.36232600X-RAY DIFFRACTION99.96
1.32-1.330.31371640.30452590X-RAY DIFFRACTION100
1.33-1.350.28921460.27752552X-RAY DIFFRACTION100
1.35-1.360.30291460.24032598X-RAY DIFFRACTION99.96
1.36-1.380.24881360.21512624X-RAY DIFFRACTION100
1.38-1.40.25651220.20262602X-RAY DIFFRACTION100
1.4-1.420.23391360.18522592X-RAY DIFFRACTION100
1.42-1.440.21851470.1772603X-RAY DIFFRACTION99.96
1.44-1.470.19051460.17152596X-RAY DIFFRACTION99.96
1.47-1.490.20221500.17722579X-RAY DIFFRACTION99.96
1.49-1.520.21711640.1892566X-RAY DIFFRACTION99.96
1.52-1.540.21021360.1782589X-RAY DIFFRACTION100
1.54-1.570.17461500.14032593X-RAY DIFFRACTION100
1.57-1.60.16641430.1432582X-RAY DIFFRACTION100
1.6-1.640.17921350.13242635X-RAY DIFFRACTION99.96
1.64-1.680.14051320.12362577X-RAY DIFFRACTION100
1.68-1.720.13371490.11832607X-RAY DIFFRACTION100
1.72-1.770.15041500.11782587X-RAY DIFFRACTION100
1.77-1.820.14841400.11762606X-RAY DIFFRACTION100
1.82-1.880.14711350.1312618X-RAY DIFFRACTION100
1.88-1.940.16521320.14572597X-RAY DIFFRACTION100
1.94-2.020.15241320.12692601X-RAY DIFFRACTION100
2.02-2.110.14351340.11532615X-RAY DIFFRACTION100
2.11-2.220.14951530.1172601X-RAY DIFFRACTION100
2.22-2.360.15811430.1272622X-RAY DIFFRACTION100
2.36-2.550.15191520.13442573X-RAY DIFFRACTION100
2.55-2.80.15231410.13472609X-RAY DIFFRACTION100
2.8-3.210.17051480.14732598X-RAY DIFFRACTION100
3.21-4.040.14261350.14062641X-RAY DIFFRACTION100
4.04-63.420.1651250.15292666X-RAY DIFFRACTION100

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