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- PDB-3kae: Cdc27 N-terminus -

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Basic information

Entry
Database: PDB / ID: 3kae
TitleCdc27 N-terminus
ComponentsPossible protein of nuclear scaffold
KeywordsPROTEIN BINDING / tetratricopeptide repeat protein
Function / homology
Function and homology information


Tetratricopeptide repeat / : / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe ...Tetratricopeptide repeat / : / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
POSSIBLE PROTEIN OF NUCLEAR SCAFFOLD
Similarity search - Component
Biological speciesEncephalitozoon cuniculi (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.298 Å
AuthorsBarford, D. / Zhang, Z. / Roe, S.M.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Molecular structure of the N-terminal domain of the APC/C subunit Cdc27 reveals a homo-dimeric tetratricopeptide repeat architecture
Authors: Zhang, Z. / Roe, S.M. / Diogon, M. / Kong, E. / El Alaoui, H. / Barford, D.
History
DepositionOct 19, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Possible protein of nuclear scaffold
B: Possible protein of nuclear scaffold
C: Possible protein of nuclear scaffold
D: Possible protein of nuclear scaffold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,2989
Polymers112,8904
Non-polymers4085
Water2,126118
1
A: Possible protein of nuclear scaffold
C: Possible protein of nuclear scaffold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7576
Polymers56,4452
Non-polymers3124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Possible protein of nuclear scaffold
D: Possible protein of nuclear scaffold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5413
Polymers56,4452
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.720, 81.890, 87.445
Angle α, β, γ (deg.)101.430, 90.070, 89.990
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'A' and (resseq 3:29 or resseq 36:162 or resseq 175:241 )A0
211chain 'B' and (resseq 3:29 or resseq 36:162 or resseq 175:241 )B0
311chain 'C' and (resseq 3:29 or resseq 36:162 or resseq 175:241 )C0
411chain 'D' and (resseq 3:29 or resseq 36:162 or resseq 175:241 )D0

NCS oper:
IDCodeMatrixVector
1given(0.986601, 0.08205, -0.141016), (-0.083189, 0.996531, -0.002194), (0.140347, 0.013895, 0.990005)19.325199, -31.714001, -44.135601
2given(0.986474, -0.08164, 0.142141), (-0.08276, -0.996567, 0.00198), (0.141492, -0.013717, -0.989844)2.11575, -30.7008, -46.2183
3given(0.999998, -0.000204, 0.002149), (-0.000205, -1, 0.000183), (0.002149, -0.000184, -0.999998)17.372299, -0.434139, 0.377239

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Components

#1: Protein
Possible protein of nuclear scaffold / Cdc27


Mass: 28222.584 Da / Num. of mol.: 4 / Fragment: N-terminal domain, residues 1-242
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Encephalitozoon cuniculi (fungus) / Gene: NC_003237 / Plasmid: pOPINS / Production host: Escherichia coli (E. coli) / References: UniProt: Q8SQV4
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.16 Å3/Da / Density % sol: 43.02 % / Mosaicity: 0.52 °

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.298→85.709 Å / Num. obs: 40000 / % possible obs: 95.5 % / Redundancy: 2.8 % / Rsym value: 0.049

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.298→53.533 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.729 / SU ML: 0.25 / σ(F): 1.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.262 2008 5.04 %
Rwork0.217 --
obs0.219 39813 94.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.203 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso max: 231.53 Å2 / Biso mean: 70.241 Å2 / Biso min: 25.34 Å2
Baniso -1Baniso -2Baniso -3
1-10.925 Å21.028 Å2-2.368 Å2
2---16.329 Å2-2.479 Å2
3---5.404 Å2
Refinement stepCycle: LAST / Resolution: 2.298→53.533 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7111 0 24 118 7253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077291
X-RAY DIFFRACTIONf_angle_d0.9689836
X-RAY DIFFRACTIONf_chiral_restr0.0691080
X-RAY DIFFRACTIONf_plane_restr0.0041256
X-RAY DIFFRACTIONf_dihedral_angle_d15.9692600
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1688X-RAY DIFFRACTIONPOSITIONAL0.054
12B1688X-RAY DIFFRACTIONPOSITIONAL0.054
13C1676X-RAY DIFFRACTIONPOSITIONAL0.056
14D1717X-RAY DIFFRACTIONPOSITIONAL0.044
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.298-2.3810.3271920.2973583377591
2.381-2.4760.3292160.2733830404695
2.476-2.5890.3111840.2443722390695
2.589-2.7250.3041940.2373818401294
2.725-2.8960.2912230.2333801402495
2.896-3.1190.3151890.2253759394894
3.119-3.4330.2821930.2123809400295
3.433-3.930.2081910.1873823401496
3.93-4.950.2422060.1923854406096
4.95-53.5470.2242200.1973806402696
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)
11.61610.588-0.75952.1838-0.1661.2362-0.05970.14160.4601-0.77470.1253-0.0387-0.4225-0.0408-0.05060.55340.0104-0.04230.26730.04170.358326.9073-6.1192-28.4702
21.68910.53440.1812.5129-1.53281.9109-0.18920.14360.2331-0.63860.09170.1685-0.0153-0.04410.10250.44320.01120.00850.24170.01160.28757.34826.233314.4307
31.4414-0.3221-0.00152.8044-1.82252.1167-0.1347-0.1371-0.22460.52530.07650.08740.0178-0.04460.070.4278-0.00850.01340.29820.0030.316524.6527-26.9051-14.1069
41.4847-0.45140.99692.1976-0.20791.1173-0.045-0.2017-0.440.79730.1544-0.11070.4044-0.0017-0.08970.5780.00160.07380.29590.02750.37449.37635.847628.8973
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN AA3 - 242
2X-RAY DIFFRACTION2CHAIN BB4 - 242
3X-RAY DIFFRACTION3CHAIN CC4 - 242
4X-RAY DIFFRACTION4CHAIN DD3 - 242

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