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- PDB-2fcq: X-ray Crystal Structure of a Chemically Synthesized Ubiquitin wit... -

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Basic information

Entry
Database: PDB / ID: 2fcq
TitleX-ray Crystal Structure of a Chemically Synthesized Ubiquitin with a Cubic Space Group
ComponentsUbiquitin
KeywordsSTRUCTURAL PROTEIN / ubiquitin
Function / homology
Function and homology information


nucleus / cytoplasm
Similarity search - Function
Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily ...Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
: / : / Polyubiquitin
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsBang, D. / Gribenko, A.V. / Tereshko, V. / Kossiakoff, A.A. / Kent, S.B. / Makhatadze, G.I.
CitationJournal: Nat.Chem.Biol. / Year: 2006
Title: Dissecting the energetics of protein alpha-helix C-cap termination through chemical protein synthesis.
Authors: Bang, D. / Gribenko, A.V. / Tereshko, V. / Kossiakoff, A.A. / Kent, S.B. / Makhatadze, G.I.
History
DepositionDec 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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 / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9049
Polymers17,1182
Non-polymers7877
Water0
1
A: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0085
Polymers8,5591
Non-polymers4504
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8964
Polymers8,5591
Non-polymers3373
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.059, 105.059, 105.059
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein Ubiquitin /


Mass: 8558.793 Da / Num. of mol.: 2 / Fragment: residues 1-76 / Mutation: M1L / Source method: obtained synthetically
Details: The protein was chemically synthesized. The sequence of the protein can be naturally found in Homo sapiens (Human)
References: GenBank: 15928840, UniProt: Q9PST8*PLUS
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cd

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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: 2.82 Å3/Da / Density % sol: 56.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.75
Details: by mixing 2 ul of ubiquitin solution (20 mg/ml) and 0.5 ul of crystallization buffer solution. The crystallization buffer was prepared by mixing 3ml of HEPES buffer (0.1M), 3ml of ...Details: by mixing 2 ul of ubiquitin solution (20 mg/ml) and 0.5 ul of crystallization buffer solution. The crystallization buffer was prepared by mixing 3ml of HEPES buffer (0.1M), 3ml of poly(ethylene glycol) 3350 (25%, w/v), and 0.2ml of 1M cadmium acetate, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 23, 2004 / Details: MIRRORS
RadiationMonochromator: SI(111) DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. obs: 3300 / % possible obs: 99.6 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 23.9
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1YIW, CHAIN B

1yiw


Resolution: 3.3→20 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.903 / SU B: 62.771 / SU ML: 0.458 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.624 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28563 293 9 %RANDOM
Rwork0.24149 ---
all0.25 ---
obs0.24617 2958 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 85 Å2
Refinement stepCycle: LAST / Resolution: 3.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1164 0 7 0 1171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221177
X-RAY DIFFRACTIONr_bond_other_d0.0010.021126
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.9231588
X-RAY DIFFRACTIONr_angle_other_deg0.7152.1092644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.635144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.62926.15452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.00715240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.22156
X-RAY DIFFRACTIONr_chiral_restr0.0670.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021256
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02194
X-RAY DIFFRACTIONr_nbd_refined0.240.2244
X-RAY DIFFRACTIONr_nbd_other0.1880.21160
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.080.2588
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.225
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2570.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2680.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2210.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it01.5971
X-RAY DIFFRACTIONr_mcbond_other01.5298
X-RAY DIFFRACTIONr_mcangle_it021190
X-RAY DIFFRACTIONr_scbond_it03515
X-RAY DIFFRACTIONr_scangle_it04.5398
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.301→3.384 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.456 19
Rwork0.333 208
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)
111.60653.6155-2.245813.8503-0.35764.21620.6578-0.43930.92130.7068-0.39660.1404-0.8834-0.0457-0.26120.00890.030.098-0.26860.0003-0.381824.865738.6469-17.3587
214.71056.2745.54835.26112.535613.06740.6636-0.7155-1.56890.1006-0.12560.41150.8681-0.7744-0.538-0.144-0.1604-0.1685-0.23580.2193-0.038237.004846.92063.5538
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 731 - 73
2X-RAY DIFFRACTION1AC - F100 - 4001
3X-RAY DIFFRACTION2BB1 - 731 - 73
4X-RAY DIFFRACTION2BG - I600 - 8001

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