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- PDB-5fby: Crystal structure of ctSPD -

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Basic information

Entry
Database: PDB / ID: 5fby
TitleCrystal structure of ctSPD
Components
  • cleaved peptide
  • separase
KeywordsHYDROLASE / cohesin / complex
Function / homology
Function and homology information


separase / meiotic chromosome separation / mitotic spindle pole body / mitotic spindle / cysteine-type endopeptidase activity / proteolysis / nucleus / cytoplasm
Similarity search - Function
Peptidase C50, separase / SEPARIN core domain / Separin, protease domain / SEPARIN core domain profile.
Similarity search - Domain/homology
Biological speciesChaetomium thermophilum (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.898 Å
AuthorsLin, Z. / Luo, X. / Yu, H.
CitationJournal: Nature / Year: 2016
Title: Structural basis of cohesin cleavage by separase.
Authors: Lin, Z. / Luo, X. / Yu, H.
History
DepositionDec 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Apr 27, 2016Group: Database references
Revision 1.3May 4, 2016Group: Structure summary
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.5Mar 6, 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: separase
B: cleaved peptide


Theoretical massNumber of molelcules
Total (without water)65,3402
Polymers65,3402
Non-polymers00
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-8 kcal/mol
Surface area21260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.559, 98.889, 107.747
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein separase


Mass: 62462.699 Da / Num. of mol.: 1 / Fragment: unp residues 1621-2223
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0070540 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SHM3
#2: Protein/peptide cleaved peptide


Mass: 2877.183 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG3350, ammonium citrate tribasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.898→50 Å / Num. obs: 47718 / % possible obs: 100 % / Redundancy: 7.2 % / Net I/σ(I): 27.7

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
Cootmodel building
HKL-3000data collection
HKL-3000phasing
RefinementResolution: 1.898→49.381 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.198 2006 4.28 %
Rwork0.1709 --
obs0.1721 46923 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.898→49.381 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3937 0 13 394 4344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114040
X-RAY DIFFRACTIONf_angle_d1.2625471
X-RAY DIFFRACTIONf_dihedral_angle_d13.5271469
X-RAY DIFFRACTIONf_chiral_restr0.052601
X-RAY DIFFRACTIONf_plane_restr0.009708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8982-1.94570.25861330.23592736X-RAY DIFFRACTION85
1.9457-1.99830.25991250.20053022X-RAY DIFFRACTION94
1.9983-2.05710.2371540.18783167X-RAY DIFFRACTION99
2.0571-2.12350.20181460.17993189X-RAY DIFFRACTION100
2.1235-2.19940.22311370.17633230X-RAY DIFFRACTION100
2.1994-2.28750.21291400.17973228X-RAY DIFFRACTION100
2.2875-2.39160.20961410.1693244X-RAY DIFFRACTION100
2.3916-2.51770.18661480.16253245X-RAY DIFFRACTION100
2.5177-2.67540.18491460.17173232X-RAY DIFFRACTION100
2.6754-2.88190.18351450.16523254X-RAY DIFFRACTION100
2.8819-3.17190.18841440.17293289X-RAY DIFFRACTION100
3.1719-3.63080.17881460.15653286X-RAY DIFFRACTION100
3.6308-4.57390.17841510.1463325X-RAY DIFFRACTION100
4.5739-49.39730.20341500.18333470X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.84030.0926-0.37290.534-0.23131.5464-0.0818-0.0448-0.2936-0.06180.0662-0.0690.4423-0.07580.10090.1872-0.0511-0.04390.08930.03340.160612.929-2.390810.5232
21.4066-0.18560.35730.3566-0.42030.8722-0.0084-0.2075-0.4005-0.1608-0.2514-0.21440.4340.486-0.34990.21650.22080.04110.37280.23960.37436.006-9.37849.9968
31.033-0.261-0.3241.3686-0.2141.39150.022-0.16070.10970.18470.0883-0.0477-0.22540.0077-0.05140.1347-0.0181-0.02630.10090.01420.089810.744817.799415.5046
42.8461-0.33721.04723.4078-0.20971.4477-0.0317-0.0620.018-0.06770.11560.1607-0.1083-0.2115-0.05410.14830.0450.0370.11680.04630.1194-1.553522.010110.8067
51.5811-0.1093-0.33651.5495-0.65471.72950.0377-0.10760.04790.11890.09530.0373-0.1605-0.12540.02980.1034-0.0072-0.03330.09110.02210.08238.823813.455418.2463
64.0944-3.2347-2.98443.74072.49822.47980.32820.6346-0.1662-0.6062-0.21230.2531-0.0381-0.45150.14360.1508-0.0356-0.05890.21070.00270.159713.6443.5653-6.0068
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1684 through 1818 )
2X-RAY DIFFRACTION2chain 'A' and (resid 1819 through 1945 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1946 through 2059 )
4X-RAY DIFFRACTION4chain 'A' and (resid 2060 through 2112 )
5X-RAY DIFFRACTION5chain 'A' and (resid 2113 through 2220 )
6X-RAY DIFFRACTION6chain 'B' and (resid 10 through 20 )

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