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- PDB-4yto: Structure of coiled-coil domain of SYCP1 -

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Basic information

Entry
Database: PDB / ID: 4yto
TitleStructure of coiled-coil domain of SYCP1
ComponentsSynaptonemal complex protein 1
KeywordsCELL CYCLE / coiled-coil domain / Syneptonemal complex / SYCP1
Function / homology
Function and homology information


transverse filament / lateral element assembly / meiotic DNA repair synthesis / chiasma assembly / autosome / central element / sperm DNA condensation / synaptonemal complex assembly / homologous chromosome pairing at meiosis / synaptonemal complex ...transverse filament / lateral element assembly / meiotic DNA repair synthesis / chiasma assembly / autosome / central element / sperm DNA condensation / synaptonemal complex assembly / homologous chromosome pairing at meiosis / synaptonemal complex / reciprocal meiotic recombination / chromosome, centromeric region / Meiotic synapsis / male germ cell nucleus / regulation of protein localization / chromosome / double-stranded DNA binding / spermatogenesis / protein homotetramerization / cell division / DNA binding
Similarity search - Function
Synaptonemal complex protein 1 / Synaptonemal complex protein 1 (SCP-1)
Similarity search - Domain/homology
Synaptonemal complex protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
Authorspark, H.H.
CitationJournal: To Be Published
Title: Structure of coiled-coil domain of SYCP1
Authors: Park, H.H.
History
DepositionMar 18, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Synaptonemal complex protein 1
B: Synaptonemal complex protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4774
Polymers35,2922
Non-polymers1842
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-28 kcal/mol
Surface area15420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.606, 119.606, 83.572
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1026-

HOH

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Components

#1: Protein Synaptonemal complex protein 1 / SCP-1 / Cancer/testis antigen 8 / CT8


Mass: 17646.160 Da / Num. of mol.: 2 / Fragment: UNP residues 662-801
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SYCP1, SCP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15431
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.23 Å3/Da / Density % sol: 70.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: ammonium chloride, 0.1 M sodium acetate / PH range: 4.6 - 5.0

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 39027 / % possible obs: 97.5 % / Redundancy: 7 % / Net I/σ(I): 30

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2→28.19 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.788 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2561 1978 4.9 %RANDOM
Rwork0.23062 ---
obs0.23188 38335 97.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.135 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 2→28.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1561 0 12 155 1728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0191579
X-RAY DIFFRACTIONr_bond_other_d0.0020.021625
X-RAY DIFFRACTIONr_angle_refined_deg2.3652.0092097
X-RAY DIFFRACTIONr_angle_other_deg1.06833782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2535190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.39727.06775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.9415368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.718156
X-RAY DIFFRACTIONr_chiral_restr0.1620.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021696
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02286
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_it5.7934.193766
X-RAY DIFFRACTIONr_mcbond_other5.7934.188765
X-RAY DIFFRACTIONr_mcangle_it7.1466.195954
X-RAY DIFFRACTIONr_mcangle_other7.1436.202955
X-RAY DIFFRACTIONr_scbond_it6.8934.872812
X-RAY DIFFRACTIONr_scbond_other6.8944.872812
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.7987.0281142
X-RAY DIFFRACTIONr_long_range_B_refined11.29133.7681979
X-RAY DIFFRACTIONr_long_range_B_other11.27333.7631979
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 146 -
Rwork0.326 2813 -
obs--99.3 %

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