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- PDB-4r3q: Crystal structure of SYCE3 -

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Basic information

Entry
Database: PDB / ID: 4r3q
TitleCrystal structure of SYCE3
ComponentsSynaptonemal complex central element protein 3
KeywordsCELL CYCLE / coiled-coil / 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 / SAD / Resolution: 1.901 Å
AuthorsLu, J. / Feng, J. / Zhou, W. / Yang, X. / Shen, Y.
CitationJournal: 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 17, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 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 central element protein 3
B: Synaptonemal complex central element protein 3


Theoretical massNumber of molelcules
Total (without water)20,9602
Polymers20,9602
Non-polymers00
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-46 kcal/mol
Surface area7890 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

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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


Mass: 18.015 Da / Num. of mol.: 70 / 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 / pH: 3.5
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
RadiationMonochromator: Si 111 CHANNEL / Protocol: 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. all: 16498 / Num. obs: 15986 / % possible obs: 96.89 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 33.16 Å2
Reflection shellResolution: 1.9→1.93 Å / % possible all: 93.94

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.901→23.661 Å / FOM work R set: 0.8305 / SU ML: 0.22 / σ(F): 0.09 / Phase error: 24.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2345 812 5.08 %RANDOM
Rwork0.2147 ---
all0.2172 16498 --
obs0.2157 15986 93.94 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.032 Å2 / ksol: 0.406 e/Å3
Displacement parametersBiso max: 98.21 Å2 / Biso mean: 45.65 Å2 / Biso min: 21.42 Å2
Baniso -1Baniso -2Baniso -3
1-4.7059 Å20 Å2-0 Å2
2--4.7059 Å20 Å2
3----9.4118 Å2
Refinement stepCycle: LAST / Resolution: 1.901→23.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1115 0 0 70 1185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071191
X-RAY DIFFRACTIONf_angle_d0.8741608
X-RAY DIFFRACTIONf_chiral_restr0.067185
X-RAY DIFFRACTIONf_plane_restr0.003204
X-RAY DIFFRACTIONf_dihedral_angle_d13.342484
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9007-2.01970.28511150.25011981209674
2.0197-2.17550.23191200.20392587270795
2.1755-2.39430.20381430.19242624276798
2.3943-2.74030.25391510.20382676282799
2.7403-3.45070.27751490.201526902839100
3.4507-23.66320.20851340.22992616275097
Refinement TLS params.Method: refined / Origin x: 31.2242 Å / Origin y: -10.5981 Å / Origin z: -0.0676 Å
111213212223313233
T0.2428 Å20.0494 Å20.0162 Å2-0.1708 Å20.0119 Å2--0.2021 Å2
L1.4529 °2-0.396 °20.8361 °2-1.7598 °20.4704 °2--1.3701 °2
S-0.1022 Å °-0.1127 Å °0.0752 Å °-0.1603 Å °0.0481 Å °-0.0034 Å °-0.3521 Å °-0.185 Å °0.0406 Å °
Refinement TLS groupSelection details: ALL

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