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- PDB-3zn3: N-terminal domain of S. pombe Cdc23 APC subunit -

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Basic information

Entry
Database: PDB / ID: 3zn3
TitleN-terminal domain of S. pombe Cdc23 APC subunit
ComponentsANAPHASE-PROMOTING COMPLEX SUBUNIT 8
KeywordsCELL CYCLE / TPR
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: 1.9 Å
AuthorsZhang, Z. / Yang, J. / Conin, N. / Kulkarni, K. / Barford, D.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: The Four Canonical Tpr Subunits of Human Apc/C Form Related Homo-Dimeric Structures and Stack in Parallel to Form a Tpr Suprahelix
Authors: Zhang, Z. / Chang, L. / Yang, J. / Conin, N. / Kulkarn, K. / Barford, D.
History
DepositionFeb 13, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2013Group: Database references
Revision 1.2May 1, 2013Group: Database references
Revision 1.3Nov 13, 2013Group: Database references
Revision 1.4Oct 30, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle ...pdbx_database_status / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_database_status.status_code_sf / _struct_conn.conn_type_id ..._pdbx_database_status.status_code_sf / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.5Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.6May 8, 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: ANAPHASE-PROMOTING COMPLEX SUBUNIT 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4734
Polymers33,8711
Non-polymers6023
Water21612
1
A: ANAPHASE-PROMOTING COMPLEX SUBUNIT 8
hetero molecules

A: ANAPHASE-PROMOTING COMPLEX SUBUNIT 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9468
Polymers67,7432
Non-polymers1,2046
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area5940 Å2
ΔGint-174.8 kcal/mol
Surface area23600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.875, 56.875, 154.814
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein ANAPHASE-PROMOTING COMPLEX SUBUNIT 8 / 20S CYCLOSOME/APC COMPLEX PROTEIN APC8 / CELL UNTIMELY TORN PROTEIN 23 / CDC23


Mass: 33871.359 Da / Num. of mol.: 1 / Fragment: RESIDUES 19-301
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHIZOSACCHAROMYCES POMBE (fission yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O94556
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 1.95 Å3/Da / Density % sol: 37.9 % / Description: NONE
Crystal growpH: 8 / Details: 200 MM SODIUM FORMATE, PH 7.5, 20% (W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→45.83 Å / Num. obs: 20943 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 23.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 18.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 18.8 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 4.8 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALEITdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.9→154.81 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.662 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.25883 676 3.2 %RANDOM
Rwork0.20568 ---
obs0.20727 20156 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20 Å20 Å2
2--0.69 Å20 Å2
3----1.37 Å2
Refinement stepCycle: LAST / Resolution: 1.9→154.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2010 0 3 12 2025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022050
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0061.972764
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3865242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.30823.85496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.35815376
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6091512
X-RAY DIFFRACTIONr_chiral_restr0.1730.2306
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021516
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 46 -
Rwork0.21 1280 -
obs--98.44 %
Refinement TLS params.Method: refined / Origin x: -3.0237 Å / Origin y: -4.4639 Å / Origin z: 26.382 Å
111213212223313233
T0.0416 Å2-0.0114 Å2-0.0216 Å2-0.0267 Å20.0021 Å2--0.0152 Å2
L0.5399 °20.0536 °2-0.1481 °2-0.3146 °2-0.1673 °2--0.7948 °2
S-0.0054 Å °0.0425 Å °0.015 Å °-0.0559 Å °0.0074 Å °0.0499 Å °0.0434 Å °-0.0303 Å °-0.002 Å °

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