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- PDB-6r2f: Crystal structure of TEX12 F102A F109E V116A in an alternative co... -

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Basic information

Entry
Database: PDB / ID: 6r2f
TitleCrystal structure of TEX12 F102A F109E V116A in an alternative conformation
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 / Testis-expressed protein 12
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsDunce, J.M. / 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: Meiotic synaptonemal complex extension through fibrous assembly of SYCE2-TEX12
Authors: Dunce, J.M. / Salmon, L.J. / Davies, O.R.
History
DepositionMar 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Testis-expressed protein 12
B: Testis-expressed protein 12
C: Testis-expressed protein 12
D: Testis-expressed protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,29517
Polymers35,9244
Non-polymers1,37113
Water2,612145
1
A: Testis-expressed protein 12
B: Testis-expressed protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3526
Polymers17,9622
Non-polymers3904
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-84 kcal/mol
Surface area9810 Å2
MethodPISA
2
C: Testis-expressed protein 12
D: Testis-expressed protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,94311
Polymers17,9622
Non-polymers9819
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-84 kcal/mol
Surface area8930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.860, 104.510, 127.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11B-117-

ILE

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Components

#1: Protein
Testis-expressed protein 12


Mass: 8981.099 Da / Num. of mol.: 4
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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.78 Å3/Da / Density % sol: 55.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M lithum nitrate, 40 % MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.29→40.41 Å / Num. obs: 18314 / % possible obs: 99.6 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.053 / Rrim(I) all: 0.144 / Net I/σ(I): 8.7
Reflection shellResolution: 2.29→2.37 Å / Rmerge(I) obs: 1.419 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1770 / Rpim(I) all: 0.552 / Rrim(I) all: 1.525

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
Aimlessdata scaling
PHASERphasing
AMPLEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ab initio models

Resolution: 2.29→40.41 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 31.02
RfactorNum. reflection% reflection
Rfree0.2621 1634 4.73 %
Rwork0.2378 --
obs0.239 18283 99.17 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å
Refinement stepCycle: LAST / Resolution: 2.29→40.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1983 0 90 145 2218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072080
X-RAY DIFFRACTIONf_angle_d0.9412798
X-RAY DIFFRACTIONf_dihedral_angle_d24.533800
X-RAY DIFFRACTIONf_chiral_restr0.047326
X-RAY DIFFRACTIONf_plane_restr0.005350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.35740.37111640.34832694X-RAY DIFFRACTION99
2.3574-2.43350.32831450.33142734X-RAY DIFFRACTION99
2.4335-2.52050.30141450.2842700X-RAY DIFFRACTION99
2.5205-2.62140.32021140.29682780X-RAY DIFFRACTION99
2.6214-2.74060.28591410.2852750X-RAY DIFFRACTION99
2.7406-2.88510.30011200.24442724X-RAY DIFFRACTION100
2.8851-3.06580.27971180.23442791X-RAY DIFFRACTION100
3.0658-3.30240.24161110.23892772X-RAY DIFFRACTION99
3.3024-3.63450.23571620.20832723X-RAY DIFFRACTION99
3.6345-4.160.23731480.19772757X-RAY DIFFRACTION100
4.16-5.23940.1921190.18212745X-RAY DIFFRACTION99
5.2394-40.42090.28671470.25532716X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.93286.87763.41738.90051.05444.51160.3244-2.4911-0.28540.2264-1.0929-1.60622.11230.8835-0.00650.5440.3753-0.03341.11260.13130.403339.365274.667299.6915
21.16480.06172.03625.06636.38699.7323-0.11370.1496-0.374-0.10150.8604-0.4452-0.22980.9019-0.64710.42860.11560.12420.6221-0.01430.506538.563364.484476.7732
31.71060.3402-0.37885.65844.82255.278-0.3006-0.75610.3626-0.49440.05880.7351-1.70470.55070.21130.67730.319-0.03950.7119-0.06360.556835.539747.718148.5695
43.89082.51743.32346.84784.42263.744-0.70571.18650.3604-0.62920.38140.3052-1.4481-0.27170.3130.62990.18760.03440.5857-0.01360.381829.625534.826131.1485
57.96530.03992.78648.53754.94094.8756-0.57370.63330.3389-0.22320.45040.12770.01462.29170.05910.44760.1310.00610.47070.02070.362639.261432.779537.6278
60.4106-2.1351-1.70637.3175.81334.28070.0374-0.04070.15220.47250.7353-0.37530.36010.5277-0.79120.5720.2671-0.02670.7354-0.08640.595237.687147.809266.8516
74.4762-3.0486-0.00463.45562.08413.8504-0.44150.4332-1.81941.3050.0170.23341.8713-0.99920.54410.60160.14620.0830.64010.00330.496132.429861.19688.1261
83.2341-1.9399-2.76027.83575.00193.928-0.53850.19070.32950.85410.3443-0.130.91310.40670.01470.40120.17330.01770.54980.09780.43829.194371.209399.4214
98.49155.34068.1896.14656.00828.2085-0.71291.09991.067-3.6227-0.0329-1.7668-3.1320.97-0.28511.32520.26530.2170.5721-0.05650.604236.862375.666770.6355
101.98251.7434-2.80761.5279-2.08317.44040.14010.41-0.0443-0.05340.18830.08140.0273-0.7786-0.36660.39370.20250.02790.4372-0.010.326926.267673.56587.3986
116.53111.3174-5.76171.56470.10866.6726-0.1563-1.9504-0.59690.2455-0.9461-0.56580.24391.5150.87720.47510.3203-0.03750.73380.15110.499510.934470.4743110.6405
126.1982.721-2.14897.6543-5.55245.04851.4998-1.0393-0.42491.0017-1.3680.3657-2.31770.9224-0.14320.90930.17580.18720.73990.1190.5827-3.420366.5366128.9489
137.84226.4721-2.75135.5346-3.10436.037-0.5283-3.24980.28671.526-0.55720.77260.3296-1.01691.17470.97310.3380.12491.0323-0.20830.4518-6.270775.9118122.0405
142.15381.208-3.361.5262-0.81636.3494-0.15890.1543-0.02660.3373-0.05520.0254-0.1148-0.06930.24120.4150.2376-0.01650.59980.02420.364.877573.1145104.2263
159.5299-0.0192-6.53351.9458-0.47364.53120.28721.3479-0.4525-0.1923-0.1827-0.0349-0.3578-1.28770.05750.40590.185-0.0330.6382-0.07060.376919.412270.433181.5417
169.5902-1.5325-5.84426.73553.25222.05610.16780.4666-0.1925-0.9318-0.59381.0375-2.0007-1.77860.25020.86270.03660.06570.5866-0.07990.427633.940366.358463.9686
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 54:58)
2X-RAY DIFFRACTION2(chain A and resid 59:87)
3X-RAY DIFFRACTION3(chain A and resid 88:103)
4X-RAY DIFFRACTION4(chain A and resid 104:117)
5X-RAY DIFFRACTION5(chain B and resid 54:70)
6X-RAY DIFFRACTION6(chain B and resid 71:96)
7X-RAY DIFFRACTION7(chain B and resid 97:105)
8X-RAY DIFFRACTION8(chain B and resid 106:117)
9X-RAY DIFFRACTION9(chain C and resid 58:65)
10X-RAY DIFFRACTION10(chain C and resid 66:84)
11X-RAY DIFFRACTION11(chain C and resid 85:103)
12X-RAY DIFFRACTION12(chain C and resid 104:115)
13X-RAY DIFFRACTION13(chain D and resid 58:66)
14X-RAY DIFFRACTION14(chain D and resid 67:85)
15X-RAY DIFFRACTION15(chain D and resid 86:103)
16X-RAY DIFFRACTION16(chain D and resid 104:116)

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