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- PDB-1gqp: APC10/DOC1 SUBUNIT OF S. cerevisiae -

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Basic information

Entry
Database: PDB / ID: 1gqp
TitleAPC10/DOC1 SUBUNIT OF S. cerevisiae
ComponentsDOC1/APC10
KeywordsCELL CYCLE / APC10/DOC1 / APC/CYCLOSOME / UBIQUITINATION / E3 UBIQUITIN LIGASE / BETA SANDWICH / JELLY ROLL
Function / homology
Function and homology information


anaphase-promoting complex / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / protein K11-linked ubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / enzyme regulator activity / regulation of mitotic cell cycle / chromatin organization / protein ubiquitination / cell division / mitochondrion
Similarity search - Function
Anaphase-promoting complex subunit APC10/Doc1 / APC10/DOC domain / Anaphase-promoting complex, subunit 10 (APC10) / DOC domain profile. / Anaphase-promoting complex, subunit 10 (APC10) / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
BROMIDE ION / Anaphase-promoting complex subunit DOC1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.2 Å
AuthorsAu, S.W.N. / Leng, X. / Harper, J.W.A.D.E. / Barford, D.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Implications for the Ubiquitination Reaction of the Anaphase-Promoting Complex from the Crystal Structure of the Doc1/Apc10 Subunit.
Authors: Au, S.W.N. / Leng, X. / Harper, J.W.A.D.E. / Barford, D.
History
DepositionNov 28, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 5, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Derived calculations / Refinement description
Category: atom_site / pdbx_struct_sheet_hbond ...atom_site / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software / struct_conf / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_seq_id / _atom_site.type_symbol / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.sheet_id / _software.name / _struct_conf.pdbx_PDB_helix_id / _struct_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.sheet_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.symmetry
Revision 2.1May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DOC1/APC10
B: DOC1/APC10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7358
Polymers51,2562
Non-polymers4796
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.065, 91.065, 114.171
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.62659, -0.77929, 0.009866), (-0.77932, -0.6264, 0.016692), (-0.006828, -0.018148, -0.99981)
Vector: 33.169, 85.438, 24.889)

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Components

#1: Protein DOC1/APC10


Mass: 25627.854 Da / Num. of mol.: 2 / Fragment: RESIDUE 63-283
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PET28M / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: P53068
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.87 %
Crystal growpH: 4.6
Details: 0.1M SODIUM ACETATE, 0.3M LITHIUM BROMIDE AND 2M SODIUM FORMATE, PH 4.6
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / pH: 4.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 Msodium acetate1reservoir
22 Msodium formate1reservoirpH4.6
315 %(v/v)glycerol1reservoir
40.3 M1reservoirLiBr

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 10, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 27256 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 18.2 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 22.9
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.28 / % possible all: 99
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 310219
Reflection shell
*PLUS
Highest resolution: 2.2 Å / % possible obs: 99 % / Rmerge(I) obs: 0.278

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SHARPphasing
CNS1.1refinement
RefinementMethod to determine structure: MIRAS / Resolution: 2.2→46.24 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1821783.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES C-TERMINAL OF 256 IN CHAINS A AND B ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1330 4.9 %RANDOM
Rwork0.213 ---
obs0.213 27256 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.9592 Å2 / ksol: 0.376842 e/Å3
Displacement parametersBiso mean: 34 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å22.85 Å20 Å2
2---0.96 Å20 Å2
3---1.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.2→46.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2961 0 6 194 3161
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.13 Å / Total num. of bins used: 6 /
RfactorNum. reflection
Rwork0.244 0
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor obs: 0.2109 / Rfactor Rfree: 0.245
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0114
X-RAY DIFFRACTIONc_angle_deg1.375
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86
LS refinement shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.28 Å

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