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- PDB-4cpc: Crystal structure of human synaptonemal complex protein SYCP3 -

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Basic information

Entry
Database: PDB / ID: 4cpc
TitleCrystal structure of human synaptonemal complex protein SYCP3
ComponentsSYNAPTONEMAL COMPLEX PROTEIN 3
KeywordsCELL CYCLE / MEIOSIS / HOMOLOGOUS RECOMBINATION / CHROMOSOME STRUCTURE / COILED-COIL / FOUR- HELIX BUNDLE
Function / homology
Function and homology information


sperm DNA condensation / synaptonemal complex / lateral element / male meiosis I / chromosome, centromeric region / spermatid development / Meiotic synapsis / meiotic cell cycle / cell division / DNA binding / nucleus
Similarity search - Function
XLR/SYCP3/FAM9 domain / : / Cor1/Xlr/Xmr conserved region
Similarity search - Domain/homology
Synaptonemal complex protein 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsSyrjanen, J.L. / Pellegrini, L. / Davies, O.R.
CitationJournal: Elife / Year: 2014
Title: A molecular model for the role of SYCP3 in meiotic chromosome organisation.
Authors: Syrjanen, J.L. / Pellegrini, L. / Davies, O.R.
History
DepositionFeb 5, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2014Group: Database references
Revision 1.2Feb 27, 2019Group: Data collection / Database references / Other
Category: citation / pdbx_database_proc / pdbx_database_status
Item: _citation.pdbx_database_id_DOI / _citation.title / _pdbx_database_status.recvd_author_approval
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SYNAPTONEMAL COMPLEX PROTEIN 3
B: SYNAPTONEMAL COMPLEX PROTEIN 3
C: SYNAPTONEMAL COMPLEX PROTEIN 3
D: SYNAPTONEMAL COMPLEX PROTEIN 3
E: SYNAPTONEMAL COMPLEX PROTEIN 3
F: SYNAPTONEMAL COMPLEX PROTEIN 3
G: SYNAPTONEMAL COMPLEX PROTEIN 3
H: SYNAPTONEMAL COMPLEX PROTEIN 3


Theoretical massNumber of molelcules
Total (without water)159,1918
Polymers159,1918
Non-polymers00
Water9,494527
1
E: SYNAPTONEMAL COMPLEX PROTEIN 3
F: SYNAPTONEMAL COMPLEX PROTEIN 3
G: SYNAPTONEMAL COMPLEX PROTEIN 3
H: SYNAPTONEMAL COMPLEX PROTEIN 3


Theoretical massNumber of molelcules
Total (without water)79,5964
Polymers79,5964
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25030 Å2
ΔGint-199.1 kcal/mol
Surface area35350 Å2
MethodPISA
2
A: SYNAPTONEMAL COMPLEX PROTEIN 3
B: SYNAPTONEMAL COMPLEX PROTEIN 3
C: SYNAPTONEMAL COMPLEX PROTEIN 3
D: SYNAPTONEMAL COMPLEX PROTEIN 3


Theoretical massNumber of molelcules
Total (without water)79,5964
Polymers79,5964
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25090 Å2
ΔGint-195 kcal/mol
Surface area34800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.140, 92.381, 103.367
Angle α, β, γ (deg.)66.53, 82.32, 76.53
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9999, -0.007858, 0.009198), (-0.007635, -0.9997, -0.02401), (0.009384, 0.02393, -0.9997)
Vector: 24.8, 211.8, 123.3)

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Components

#1: Protein
SYNAPTONEMAL COMPLEX PROTEIN 3 / SCP-3


Mass: 19898.879 Da / Num. of mol.: 8 / Fragment: RESIDUES 66-230
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 DERIVATIVE / References: UniProt: Q8IZU3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / 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: 2.87 Å3/Da / Density % sol: 54.7 %
Description: DATA WERE MERGED FROM DATA-SETS COLLECTED AT THREE POINTS ALONG A SINGLE CRYSTAL.
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLISED FROM 100 MM HEPES PH 7.5, 100 MM NACL, 13.0% (W/V) PEG3350; THEN SOAKED IN 20% GLYCEROL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.9074
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2012 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.9074 Å / Relative weight: 1
ReflectionResolution: 2.24→47.36 Å / Num. obs: 66412 / % possible obs: 86.7 % / Observed criterion σ(I): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 35.48 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 11
Reflection shellResolution: 2.24→2.29 Å / Redundancy: 8.1 % / Rmerge(I) obs: 1.09 / Mean I/σ(I) obs: 2.5 / % possible all: 38.9

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
BUSTER-TNTphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SAD SOLUTION OF THE IODIDE DERVIATIVE STRUCTURE

Resolution: 2.24→47.36 Å / Cor.coef. Fo:Fc: 0.8497 / Cor.coef. Fo:Fc free: 0.8194 / SU R Cruickshank DPI: 0.298 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.291 / SU Rfree Blow DPI: 0.207 / SU Rfree Cruickshank DPI: 0.211
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2262 3301 4.97 %RANDOM
Rwork0.1953 ---
obs0.1968 66411 85.26 %-
Displacement parametersBiso mean: 61.34 Å2
Baniso -1Baniso -2Baniso -3
1-10.017 Å2-4.6158 Å2-4.3874 Å2
2---40.8688 Å2-14.2862 Å2
3---30.8518 Å2
Refinement stepCycle: LAST / Resolution: 2.24→47.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9810 0 0 527 10337
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019998HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0313308HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4082SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes417HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1305HARMONIC5
X-RAY DIFFRACTIONt_it9998HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.1
X-RAY DIFFRACTIONt_other_torsion19.98
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1270SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11541SEMIHARMONIC4
LS refinement shellResolution: 2.24→2.3 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2701 102 5.42 %
Rwork0.2447 1781 -
all0.246 1883 -
obs--85.26 %

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