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- PDB-1yj1: X-ray Crystal Structure of a Chemically Synthesized [D-Gln35]Ubiquitin -

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Basic information

Entry
Database: PDB / ID: 1yj1
TitleX-ray Crystal Structure of a Chemically Synthesized [D-Gln35]Ubiquitin
ComponentsUbiquitin
KeywordsSTRUCTURAL PROTEIN / Ubiquitin
Function / homologyPhosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Roll / Alpha Beta / : / :
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsBang, D. / Makhatadze, G.I. / Tereshko, V. / Kossiakoff, A.A. / Kent, S.B.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2005
Title: X-ray Crystal Structure of a Chemically Synthesized [D-Gln35]Ubiquitin
Authors: Bang, D. / Makhatadze, G.I. / Tereshko, V. / Kossiakoff, A.A. / Kent, S.B.
History
DepositionJan 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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 23, 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

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Assembly

Deposited unit
A: Ubiquitin
B: Ubiquitin
C: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,90723
Polymers25,8903
Non-polymers2,01720
Water4,107228
1
A: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,48810
Polymers8,6301
Non-polymers8589
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3408
Polymers8,6301
Non-polymers7107
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0805
Polymers8,6301
Non-polymers4504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-129 kcal/mol
Surface area12120 Å2
MethodPISA
5
B: Ubiquitin
hetero molecules

A: Ubiquitin
hetero molecules

C: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,90723
Polymers25,8903
Non-polymers2,01720
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-x+3/2,-y,z-1/21
crystal symmetry operation2_664-x+3/2,-y+1,z-1/21
Buried area4140 Å2
ΔGint-120 kcal/mol
Surface area11390 Å2
MethodPISA
6
A: Ubiquitin
hetero molecules

B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,82718
Polymers17,2602
Non-polymers1,56816
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+3/2,-y,z+1/21
Buried area2050 Å2
ΔGint-75 kcal/mol
Surface area8070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.872, 50.395, 92.941
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Ubiquitin


Mass: 8629.870 Da / Num. of mol.: 3 / 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
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.1 Å3/Da / Density % sol: 41.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: CdCl2, PEG MME 2000 (w/v), pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 23, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.3→20 Å / Num. all: 51444 / Num. obs: 41081 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.3→1.4 Å / % possible all: 35

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1UBQ

1ubq


Resolution: 1.3→20 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.077 / SU ML: 0.04 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21769 2096 5.1 %RANDOM
Rwork0.19522 ---
obs0.19637 38985 79.86 %-
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: 7.427 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20 Å20 Å2
2--0.39 Å20 Å2
3---0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1745 0 20 228 1993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221783
X-RAY DIFFRACTIONr_bond_other_d0.0010.021692
X-RAY DIFFRACTIONr_angle_refined_deg1.7061.9772404
X-RAY DIFFRACTIONr_angle_other_deg1.80633988
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4975214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.32426.34182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55115366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.741159
X-RAY DIFFRACTIONr_chiral_restr0.170.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021892
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02289
X-RAY DIFFRACTIONr_nbd_refined0.2670.2314
X-RAY DIFFRACTIONr_nbd_other0.1880.21693
X-RAY DIFFRACTIONr_nbtor_other0.0870.21046
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2610.2124
X-RAY DIFFRACTIONr_metal_ion_refined0.1380.219
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3010.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2410.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2960.234
X-RAY DIFFRACTIONr_mcbond_it1.6521.51445
X-RAY DIFFRACTIONr_mcbond_other0.3741.5440
X-RAY DIFFRACTIONr_mcangle_it1.90221784
X-RAY DIFFRACTIONr_scbond_it3.2353812
X-RAY DIFFRACTIONr_scangle_it4.0474.5620
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.318 35
Rwork0.266 606
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)
10.5317-0.15040.03170.8911-0.10570.7165-0.0037-0.0732-0.010.04550.0114-0.0153-0.00350.0091-0.0077-0.0173-0.00430.0059-0.009-0.0049-0.014433.33542.316810.8989
20.37920.12420.01650.7218-0.0191.2435-0.01040.06950.0113-0.05110.00620.01880.041-0.01720.0041-0.01740.0015-0.0085-0.01530.002-0.009633.13558.7327-14.7219
30.63450.1474-0.00791.08390.17911.1089-0.0231-0.02570.044-0.00350.0080.0287-0.06060.01490.0151-0.01790.0062-0.0003-0.0158-0.0026-0.015733.041127.45824.7098
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 71
2X-RAY DIFFRACTION1A90 - 119
3X-RAY DIFFRACTION1A1101 - 1163
4X-RAY DIFFRACTION2B1 - 72
5X-RAY DIFFRACTION2B201 - 229
6X-RAY DIFFRACTION2B1201 - 1262
7X-RAY DIFFRACTION3C1 - 74
8X-RAY DIFFRACTION3C304 - 325
9X-RAY DIFFRACTION3C1302 - 1369

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