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- PDB-6hk9: Crystal structure of TEX12 F102A F109E V116A -

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Basic information

Entry
Database: PDB / ID: 6hk9
TitleCrystal structure of TEX12 F102A F109E V116A
ComponentsTestis-expressed protein 12
KeywordsSTRUCTURAL PROTEIN / Synaptonemal complex / meiosis / recombination / coiled-coil / self-assembly / TEX12
Function / homologyTestis-expressed sequence 12 protein / Testis-expressed 12 / meiotic DNA repair synthesis / central element / synaptonemal complex assembly / Meiotic synapsis / chromosome / ACETATE ION / Testis-expressed protein 12
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.454 Å
AuthorsDunce, J.M. / Salmon, L.J. / Davies, O.R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust104158/Z/14/Z United Kingdom
Royal SocietyRG170118 United Kingdom
CitationJournal: To Be Published
Title: Synaptonemal complex central element extension through hierarchical assembly of SYCE2-TEX12 into alpha-fibres
Authors: Salmon, L.J. / Dunce, J.M. / Davies, O.R.
History
DepositionSep 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Testis-expressed protein 12
B: Testis-expressed protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,47912
Polymers17,9622
Non-polymers51710
Water3,603200
1
A: Testis-expressed protein 12
B: Testis-expressed protein 12
hetero molecules

A: Testis-expressed protein 12
B: Testis-expressed protein 12
hetero molecules


  • defined by author&software
  • Evidence: SAXS, Forms a homotetramer in solution through C-terminal sites (which mediate lattice-like assembly in the crystal) mediating lateral dimer-of-dimer interactions of the homodimer of the ...Evidence: SAXS, Forms a homotetramer in solution through C-terminal sites (which mediate lattice-like assembly in the crystal) mediating lateral dimer-of-dimer interactions of the homodimer of the asymmetric unit., light scattering, Forms a homotetramer in solution through C-terminal sites (which mediate lattice-like assembly in the crystal) mediating lateral dimer-of-dimer interactions of the homodimer of the asymmetric unit.
  • 37 kDa, 4 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)36,95824
Polymers35,9244
Non-polymers1,03420
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+3/21
Buried area8730 Å2
ΔGint-170 kcal/mol
Surface area22980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.233, 219.712, 37.501
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-203-

CA

21B-201-

CA

31A-372-

HOH

41A-405-

HOH

51B-329-

HOH

61B-380-

HOH

71B-386-

HOH

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Components

#1: Protein Testis-expressed protein 12


Mass: 8981.099 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TEX12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BXU0
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 200 mM Calcium acetate, 40% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.45→54.93 Å / Num. obs: 59176 / % possible obs: 98.1 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rpim(I) all: 0.017 / Rrim(I) all: 0.044 / Net I/σ(I): 20.3
Reflection shellResolution: 1.45→1.48 Å / Mean I/σ(I) obs: 2.6 / CC1/2: 0.993 / Rpim(I) all: 0.17 / Rrim(I) all: 0.472 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX(dev_3126: ???)refinement
XDSdata reduction
Aimlessdata scaling
AMPLEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Quark decoys

Resolution: 1.454→30.971 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 24.81
RfactorNum. reflection% reflection
Rfree0.2047 2931 4.95 %
Rwork0.1795 --
obs0.1808 59176 97.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.454→30.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1223 0 23 200 1446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081345
X-RAY DIFFRACTIONf_angle_d0.8561820
X-RAY DIFFRACTIONf_dihedral_angle_d19.941530
X-RAY DIFFRACTIONf_chiral_restr0.051206
X-RAY DIFFRACTIONf_plane_restr0.005245
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4537-1.47760.35821130.32772573X-RAY DIFFRACTION93
1.4776-1.5030.35661120.29812543X-RAY DIFFRACTION91
1.503-1.53040.24241440.24682601X-RAY DIFFRACTION96
1.5304-1.55980.27391420.22582603X-RAY DIFFRACTION95
1.5598-1.59160.23041450.2032686X-RAY DIFFRACTION98
1.5916-1.62630.21951230.1872678X-RAY DIFFRACTION96
1.6263-1.66410.1571360.17782706X-RAY DIFFRACTION99
1.6641-1.70570.21451470.1772661X-RAY DIFFRACTION96
1.7057-1.75180.2061610.17262673X-RAY DIFFRACTION99
1.7518-1.80340.21941480.15892703X-RAY DIFFRACTION98
1.8034-1.86160.24191760.15782643X-RAY DIFFRACTION99
1.8616-1.92810.20621200.1652759X-RAY DIFFRACTION99
1.9281-2.00530.20861260.16662703X-RAY DIFFRACTION98
2.0053-2.09650.20951350.15732701X-RAY DIFFRACTION98
2.0965-2.2070.22071220.16392761X-RAY DIFFRACTION99
2.207-2.34520.21291450.15332702X-RAY DIFFRACTION99
2.3452-2.52620.1651330.15882703X-RAY DIFFRACTION98
2.5262-2.78030.19981720.16122694X-RAY DIFFRACTION99
2.7803-3.18230.20431420.16412729X-RAY DIFFRACTION99
3.1823-4.0080.1691400.17042703X-RAY DIFFRACTION99
4.008-30.97820.22111490.2152720X-RAY DIFFRACTION98

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