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- PDB-5iwz: Synaptonemal complex protein -

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Basic information

Entry
Database: PDB / ID: 5iwz
TitleSynaptonemal complex protein
ComponentsSynaptonemal complex protein 2
KeywordsCELL CYCLE / component of synaptonemal complexes
Function / homology
Function and homology information


male genitalia morphogenesis / male meiotic nuclear division / female meiotic nuclear division / synaptonemal complex / lateral element / condensed chromosome, centromeric region / fertilization / negative regulation of reproductive process / negative regulation of developmental process / ectopic germ cell programmed cell death ...male genitalia morphogenesis / male meiotic nuclear division / female meiotic nuclear division / synaptonemal complex / lateral element / condensed chromosome, centromeric region / fertilization / negative regulation of reproductive process / negative regulation of developmental process / ectopic germ cell programmed cell death / animal organ morphogenesis / cell division / negative regulation of apoptotic process / apoptotic process / DNA binding / nucleoplasm
Similarity search - Function
Synaptonemal complex protein 2-like / Synaptonemal complex protein 2, Spt16M-like domain / Synaptonemal complex protein 2, armadillo-repeat-like domain / Synaptonemal complex 2 armadillo-repeat-like domain / Synaptonemal complex 2 Spt16M-like domain
Similarity search - Domain/homology
Synaptonemal complex protein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.098 Å
AuthorsFeng, J. / Fu, S. / Cao, X. / Wu, H. / Lu, J. / Zeng, M. / Liu, L. / Yang, X. / Shen, Y.
Funding support China, 1items
OrganizationGrant numberCountry
China
CitationJournal: To Be Published
Title: Structure of synaptonemal complexes protein at 2.6 angstroms resolution
Authors: Feng, J. / Fu, S. / Cao, X. / Wu, H. / Lu, J. / Zeng, M. / Liu, L. / Yang, X. / Shen, Y.
History
DepositionMar 23, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Mar 20, 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
A: Synaptonemal complex protein 2


Theoretical massNumber of molelcules
Total (without water)46,5791
Polymers46,5791
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.781, 74.679, 80.511
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Synaptonemal complex protein 2 / SCP-2 / Synaptonemal complex lateral element protein


Mass: 46578.828 Da / Num. of mol.: 1 / Fragment: UNP residues 1-390
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sycp2, Scp2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9CUU3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.12 Å3/Da / Density % sol: 42.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M Tris-HCl pH 6.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 23639 / % possible obs: 99.9 % / Redundancy: 7 % / Net I/σ(I): 20

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
PHENIXmodel building
HKL-2000data scaling
RefinementResolution: 2.098→32.473 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2389 1206 5.11 %
Rwork0.1904 --
obs0.1929 23596 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.098→32.473 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2961 0 0 109 3070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083001
X-RAY DIFFRACTIONf_angle_d1.4754036
X-RAY DIFFRACTIONf_dihedral_angle_d21.2411134
X-RAY DIFFRACTIONf_chiral_restr0.091473
X-RAY DIFFRACTIONf_plane_restr0.005508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.098-2.1820.27771160.21452459X-RAY DIFFRACTION99
2.182-2.28130.281440.20782444X-RAY DIFFRACTION99
2.2813-2.40150.24451380.19892459X-RAY DIFFRACTION100
2.4015-2.55190.28131360.20682481X-RAY DIFFRACTION99
2.5519-2.74890.26821270.20212480X-RAY DIFFRACTION100
2.7489-3.02530.25691470.21152481X-RAY DIFFRACTION100
3.0253-3.46270.23571410.18582507X-RAY DIFFRACTION100
3.4627-4.36090.21761300.16812538X-RAY DIFFRACTION99
4.3609-32.47660.21151270.18692541X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: -7.0497 Å / Origin y: -15.0477 Å / Origin z: 19.144 Å
111213212223313233
T0.2429 Å2-0.0454 Å2-0.0218 Å2-0.2025 Å20.0179 Å2--0.2029 Å2
L2.2144 °2-0.4019 °2-0.3638 °2-0.4589 °2-0.0527 °2--0.8056 °2
S0.0402 Å °-0.4362 Å °-0.0683 Å °0.0785 Å °0.007 Å °-0.0235 Å °-0.0841 Å °0.1149 Å °-0.0347 Å °
Refinement TLS groupSelection details: all

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