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- PDB-5fc2: Structure of a separase in complex with a pAMK peptide containing... -

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Basic information

Entry
Database: PDB / ID: 5fc2
TitleStructure of a separase in complex with a pAMK peptide containing a phospho-serine
Components
  • pAMK, peptide containing a phospho-serine
  • separase
Keywordshydrolase/hydrolase inhibitor / cohesin / complex / HYDROLASE / hydrolase-hydrolase inhibitor 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 family C50 / Peptidase C50, separase / SEPARIN core domain / SEPARIN core domain profile.
Similarity search - Domain/homology
pAMK, peptide inhibitor containing a phospho-serine / separase
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.84 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: Derived calculations / Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: pAMK, peptide containing a phospho-serine
B: separase


Theoretical massNumber of molelcules
Total (without water)61,1222
Polymers61,1222
Non-polymers00
Water8,179454
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-0 kcal/mol
Surface area21210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.354, 85.013, 119.268
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/peptide pAMK, peptide containing a phospho-serine


Type: Oligopeptide / Class: Inhibitor / Mass: 1145.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
References: pAMK, peptide inhibitor containing a phospho-serine
#2: Protein separase


Mass: 59976.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0070540 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SHM3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.35 Å3/Da / Density % sol: 47.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: pentaerythritol propoxylate (5/4 PO/OH), KCl, HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.838→50 Å / Num. obs: 50208 / % possible obs: 100 % / Redundancy: 7.5 % / Net I/σ(I): 19.8

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-3000data collection
Cootmodel building
PHENIXphasing
RefinementResolution: 1.84→42.51 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.207 1981 3.95 %
Rwork0.18 --
obs0.181 50140 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.84→42.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3864 0 0 454 4318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133956
X-RAY DIFFRACTIONf_angle_d1.0475343
X-RAY DIFFRACTIONf_dihedral_angle_d19.8541444
X-RAY DIFFRACTIONf_chiral_restr0.077588
X-RAY DIFFRACTIONf_plane_restr0.005689
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8378-1.88380.2841230.28052916X-RAY DIFFRACTION85
1.8838-1.93470.28761410.24033431X-RAY DIFFRACTION100
1.9347-1.99160.25641400.21233418X-RAY DIFFRACTION100
1.9916-2.05590.221410.18813427X-RAY DIFFRACTION100
2.0559-2.12940.18981420.18843465X-RAY DIFFRACTION100
2.1294-2.21460.22951400.1833417X-RAY DIFFRACTION100
2.2146-2.31540.19841430.17353462X-RAY DIFFRACTION100
2.3154-2.43750.22491420.17873449X-RAY DIFFRACTION100
2.4375-2.59020.20881410.1753453X-RAY DIFFRACTION100
2.5902-2.79010.21321430.18783470X-RAY DIFFRACTION100
2.7901-3.07080.2461430.17913492X-RAY DIFFRACTION100
3.0708-3.5150.17661440.16493517X-RAY DIFFRACTION100
3.515-4.42780.16641460.15193543X-RAY DIFFRACTION100
4.4278-42.51790.20331520.18393699X-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)
11.84880.5753-0.24671.16340.40631.3052-0.02960.15620.0622-0.20130.1199-0.0148-0.24560.1745-0.08620.10570.0193-0.00650.086-0.00160.1229-11.68255.1246-11.5915
21.70430.4686-0.71590.78120.02051.2801-0.18370.1734-0.1867-0.09280.11470.0340.2574-0.06190.10740.1861-0.01510.00260.1305-0.02740.1617-20.0754-11.5539-11.8743
31.7826-0.06821.02051.1637-0.42692.4270.05470.044-0.0284-0.0277-0.0863-0.11210.28680.29270.04110.14760.0246-0.01570.1808-0.00320.15068.467-6.8032-17.927
40.8470.166-0.35820.57770.00181.3437-0.0204-0.00670.06870.00020.0641-0.0275-0.09270.1269-0.03320.095-0.012-0.00630.0875-0.01240.1187-16.20825.56960.6783
51.86640.19410.05521.63830.04911.6096-0.02540.110.1574-0.09670.03260.0949-0.179-0.0798-0.0150.1180.01770.00290.0988-0.0010.1246-28.65719.27217.0149
61.79380.4670.13511.64640.12961.6881-0.0049-0.162-0.08090.13830.0459-0.04790.03820.0666-0.02930.08370.01440.00270.1050.00060.0996-17.7378-0.49936.2259
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:9 ) OR ( CHAIN B AND RESID 1697:1730 )A1 - 9
2X-RAY DIFFRACTION1( CHAIN A AND RESID 1:9 ) OR ( CHAIN B AND RESID 1697:1730 )B1697 - 1730
3X-RAY DIFFRACTION2( CHAIN B AND RESID 1731:1818 )B1731 - 1818
4X-RAY DIFFRACTION3( CHAIN B AND RESID 1819:1952 )B1819 - 1952
5X-RAY DIFFRACTION4( CHAIN B AND RESID 1953:2041 )B1953 - 2041
6X-RAY DIFFRACTION5( CHAIN B AND RESID 2042:2128 )B2042 - 2128
7X-RAY DIFFRACTION6( CHAIN B AND RESID 2129:2221 )B2129 - 2221

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