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- PDB-6h86: Rebuilt and re-refined PDB entry 4R3Q: Crystal structure of SYCE3 -

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Basic information

Entry
Database: PDB / ID: 6h86
TitleRebuilt and re-refined PDB entry 4R3Q: Crystal structure of SYCE3
ComponentsSynaptonemal complex central element protein 3
KeywordsSTRUCTURAL PROTEIN / Meiosis / synaptonemal complex
Function / homology
Function and homology information


positive regulation of developmental process / central element / positive regulation of reproductive process / synaptonemal complex assembly / reciprocal meiotic recombination / ectopic germ cell programmed cell death / chromosome / spermatogenesis / positive regulation of apoptotic process / cell division ...positive regulation of developmental process / central element / positive regulation of reproductive process / synaptonemal complex assembly / reciprocal meiotic recombination / ectopic germ cell programmed cell death / chromosome / spermatogenesis / positive regulation of apoptotic process / cell division / apoptotic process / nucleoplasm / nucleus
Similarity search - Function
Synaptonemal complex central element protein 3 / Synaptonemal complex central element protein 3
Similarity search - Domain/homology
Synaptonemal complex central element protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.901 Å
AuthorsDavies, O.R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust104158/Z/14/Z United Kingdom
Royal SocietyRG170118 United Kingdom
Citation
Journal: J.Biol.Chem. / Year: 2019
Title: A molecular model for self-assembly of the synaptonemal complex protein SYCE3.
Authors: Dunne, O.M. / Davies, O.R.
#1: Journal: Sci Rep / Year: 2014
Title: Structural insight into the central element assembly of the synaptonemal complex.
Authors: Lu, J. / Gu, Y. / Feng, J. / Zhou, W. / Yang, X. / Shen, Y.
History
DepositionAug 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 15, 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

Downloads & links

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Assembly

Deposited unit
A: Synaptonemal complex central element protein 3
B: Synaptonemal complex central element protein 3


Theoretical massNumber of molelcules
Total (without water)20,9602
Polymers20,9602
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, SEC-SAXS ab initio envelope conforms the dimeric structure, light scattering, SEC-MALS confirms a dimeric structure
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-49 kcal/mol
Surface area9070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.576, 75.576, 101.511
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-126-

HOH

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Components

#1: Protein Synaptonemal complex central element protein 3 / Testis-specific expressed protein 2 / TSEG-2


Mass: 10480.013 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Syce3, Tseg2 / Production host: Escherichia coli (E. coli) / References: UniProt: B5KM66
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.66 Å3/Da / Density % sol: 53.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1M Citric acid, 7% 2-propanol, 1% PEG 20000, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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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: Jun 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 16498 / % possible obs: 96.89 % / Redundancy: 3.9 % / Rsym value: 0.059 / Net I/σ(I): 22
Reflection shellResolution: 1.9→1.93 Å / Rsym value: 0.486

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Processing

Software
NameVersionClassification
PHENIX(1.13_2997: ???)refinement
PHENIXmodel building
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
RefinementResolution: 1.901→23.661 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 25.32
RfactorNum. reflection% reflection
Rfree0.2167 830 5.05 %
Rwork0.1922 --
obs0.1934 16432 96.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.901→23.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1258 0 0 73 1331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161340
X-RAY DIFFRACTIONf_angle_d1.2321810
X-RAY DIFFRACTIONf_dihedral_angle_d17.67880
X-RAY DIFFRACTIONf_chiral_restr0.05202
X-RAY DIFFRACTIONf_plane_restr0.007232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9007-2.01970.28711240.25952232X-RAY DIFFRACTION83
2.0197-2.17550.24371270.21052699X-RAY DIFFRACTION99
2.1755-2.39430.19621450.1922667X-RAY DIFFRACTION100
2.3943-2.74030.22221520.18282692X-RAY DIFFRACTION100
2.7403-3.45070.24411490.19282695X-RAY DIFFRACTION100
3.4507-23.66320.19471330.18632617X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 31.5493 Å / Origin y: -11.0764 Å / Origin z: -0.2192 Å
111213212223313233
T0.1974 Å20.0307 Å20.0159 Å2-0.1543 Å20.0051 Å2--0.3206 Å2
L1.3911 °2-0.6777 °20.1131 °2-2.1868 °2-0.1001 °2--6.5242 °2
S-0.1082 Å °-0.1374 Å °0.0465 Å °-0.1162 Å °0.045 Å °-0.012 Å °-0.348 Å °-0.193 Å °0.0897 Å °
Refinement TLS groupSelection details: all

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