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Basic information

Entry
Database: PDB / ID: 5ftp
Titlesulfur SAD phasing of Cdc23Nterm: data collection with a tailored X- ray beam size at 2.69 A wavelength (4.6 keV)
ComponentsANAPHASE-PROMOTING COMPLEX SUBUNIT 8
KeywordsCELL CYCLE / SAD PHASING / SULFUR / SOFT X-RAYS / LONG WAVELENGTH / LOW RESOLUTION
Function / homology
Function and homology information


Senescence-Associated Secretory Phenotype (SASP) / Regulation of APC/C activators between G1/S and early anaphase / : / Antigen processing: Ubiquitination & Proteasome degradation / mitotic sister chromatid separation / mitotic spindle pole body / anaphase-promoting complex / anaphase-promoting complex-dependent catabolic process / positive regulation of mitotic metaphase/anaphase transition / protein ubiquitination ...Senescence-Associated Secretory Phenotype (SASP) / Regulation of APC/C activators between G1/S and early anaphase / : / Antigen processing: Ubiquitination & Proteasome degradation / mitotic sister chromatid separation / mitotic spindle pole body / anaphase-promoting complex / anaphase-promoting complex-dependent catabolic process / positive regulation of mitotic metaphase/anaphase transition / protein ubiquitination / cell division / nucleus
Similarity search - Function
Tetratricopeptide repeat / Cdc23 / Anaphase promoting complex subunit 8 / Cdc23 / Tetratricopeptide repeat domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...Tetratricopeptide repeat / Cdc23 / Anaphase promoting complex subunit 8 / Cdc23 / 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
Anaphase-promoting complex subunit 8
Similarity search - Component
Biological speciesSCHIZOSACCHAROMYCES POMBE (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsCianci, M. / Groves, M.R. / Barford, D. / Schneider, T.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2016
Title: Data Collection with a Tailored X-Ray Beam Size at 2.69 A Wavelength (4.6 Kev): Sulfur Sad Phasing of Cdc23Nterm
Authors: Cianci, M. / Groves, M.R. / Barford, D. / Schneider, T.R.
History
DepositionJan 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Data collection / Category: diffrn_detector / diffrn_source
Item: _diffrn_detector.type / _diffrn_source.pdbx_synchrotron_site
Revision 1.3May 8, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANAPHASE-PROMOTING COMPLEX SUBUNIT 8
B: ANAPHASE-PROMOTING COMPLEX SUBUNIT 8


Theoretical massNumber of molelcules
Total (without water)67,7392
Polymers67,7392
Non-polymers00
Water1267
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-28.7 kcal/mol
Surface area23320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.249, 61.249, 151.559
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 21 - 284 / Label seq-ID: 4 - 267

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 8 / 20S CYCLOSOME/APC COMPLEX PROTEIN APC8 / CELL UNTIMELY TORN PROTEIN 23 / 20S CYCLOSOME/APC COMPLEX ...20S CYCLOSOME/APC COMPLEX PROTEIN APC8 / CELL UNTIMELY TORN PROTEIN 23 / 20S CYCLOSOME/APC COMPLEX PROTEIN APC8 / CELL UNTIMELY TORN PROTEIN 23


Mass: 33869.430 Da / Num. of mol.: 2 / Fragment: N-TERM, UNP RESIDUES 19-301
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHIZOSACCHAROMYCES POMBE (fission yeast)
Description: SOURCE DETAILS ARE THE SAME AS 3ZN3 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O94556
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.62 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growDetails: CRYSTALLIZATION DETAILS AS PER 3ZN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 2.69
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 10, 2012
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.69 Å / Relative weight: 1
ReflectionResolution: 3.1→61.25 Å / Num. obs: 282255 / % possible obs: 99.7 % / Observed criterion σ(I): 4.8 / Redundancy: 27.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 30.1
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 17.8 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 4.8 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
SCALAdata scaling
SHELXDphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 3.1→61.25 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.865 / SU B: 21.509 / SU ML: 0.378 / Cross valid method: THROUGHOUT / ESU R Free: 0.519 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25963 510 5 %RANDOM
Rwork0.18689 ---
obs0.19046 9615 99.73 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 3.1→61.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3859 0 0 7 3866
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193936
X-RAY DIFFRACTIONr_bond_other_d0.0050.023763
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.9715309
X-RAY DIFFRACTIONr_angle_other_deg1.45138662
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4975465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.57323.702181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.7815723
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3391523
X-RAY DIFFRACTIONr_chiral_restr0.0760.2591
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024332
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02919
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.0995.3571881
X-RAY DIFFRACTIONr_mcbond_other5.0965.3571880
X-RAY DIFFRACTIONr_mcangle_it7.6078.0232339
X-RAY DIFFRACTIONr_mcangle_other7.6078.0232340
X-RAY DIFFRACTIONr_scbond_it5.6945.9012055
X-RAY DIFFRACTIONr_scbond_other5.6825.8982053
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.8978.6492970
X-RAY DIFFRACTIONr_long_range_B_refined12.67150.9616271
X-RAY DIFFRACTIONr_long_range_B_other12.67150.9616271
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 23878 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.18 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.098→3.179 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.458 50 -
Rwork0.309 661 -
obs--96.87 %

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