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- PDB-1yiw: X-ray Crystal Structure of a Chemically Synthesized Ubiquitin -

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Basic information

Entry
Database: PDB / ID: 1yiw
TitleX-ray Crystal Structure of a Chemically Synthesized Ubiquitin
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: 1.39 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 / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_database_remark ...database_2 / pdbx_database_remark / 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_database_remark.text / _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.pdbx_dist_value / _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 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 600HETEROGEN CD90, CL91-93, HOH 94-97 ARE ASSOCIATED WITH CHAIN A, B, C. LIGANDS 101-124 ARE ...HETEROGEN CD90, CL91-93, HOH 94-97 ARE ASSOCIATED WITH CHAIN A, B, C. LIGANDS 101-124 ARE ASSOCIATED WITH CHAIN A. LIGANDS 201-229 ARE ASSOCIATED WITH CHAIN B. LIGANDS 301-328 ARE ASSOCIATED WITH CHAIN C.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)27,69423
Polymers25,6763
Non-polymers2,01720
Water4,035224
1
A: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3819
Polymers8,5591
Non-polymers8228
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2698
Polymers8,5591
Non-polymers7107
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0446
Polymers8,5591
Non-polymers4855
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-130 kcal/mol
Surface area11950 Å2
MethodPISA
5
B: Ubiquitin
hetero molecules

A: Ubiquitin
hetero molecules

C: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,69423
Polymers25,6763
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 area4160 Å2
ΔGint-124 kcal/mol
Surface area11210 Å2
MethodPISA
6
A: Ubiquitin
hetero molecules

B: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,65017
Polymers17,1182
Non-polymers1,53215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+3/2,-y,z+1/21
Buried area2050 Å2
ΔGint-76 kcal/mol
Surface area7830 Å2
MethodPISA
7
C: Ubiquitin
hetero molecules

A: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,42515
Polymers17,1182
Non-polymers1,30713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area1930 Å2
ΔGint-66 kcal/mol
Surface area8290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.776, 50.476, 92.649
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: 8558.793 Da / Num. of mol.: 3 / Mutation: M1L / Source method: obtained synthetically
Details: The sequence of this protein naturally exists in Homo sapiens (human).
References: GenBank: 15928840, UniProt: Q9PST8*PLUS
#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 / Chloride


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


Mass: 18.015 Da / Num. of mol.: 224 / 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 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.97926 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 17, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.39→20 Å / Num. all: 42005 / Num. obs: 27173 / % possible obs: 64.69 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.39→1.55 Å / % possible all: 19.1

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
MAR345data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→20 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.067 / SU ML: 0.039 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.093 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20702 1377 5.1 %RANDOM
Rwork0.171 ---
all0.1728 42005 --
obs0.17282 25796 64.69 %-
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: 10.358 Å2
Baniso -1Baniso -2Baniso -3
1--0.71 Å20 Å20 Å2
2---0.53 Å20 Å2
3---1.24 Å2
Refinement stepCycle: LAST / Resolution: 1.39→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1719 0 20 224 1963
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221742
X-RAY DIFFRACTIONr_bond_other_d00.021654
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9862351
X-RAY DIFFRACTIONr_angle_other_deg1.70333890
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6185213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67326.4178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.50615354
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.743158
X-RAY DIFFRACTIONr_chiral_restr0.0890.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021864
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02284
X-RAY DIFFRACTIONr_nbd_refined0.2640.2277
X-RAY DIFFRACTIONr_nbd_other0.20.21590
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0880.2959
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2190.2118
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2580.212
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3740.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2540.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6691.51430
X-RAY DIFFRACTIONr_mcbond_other0.0421.5441
X-RAY DIFFRACTIONr_mcangle_it1.86521762
X-RAY DIFFRACTIONr_scbond_it3.4223782
X-RAY DIFFRACTIONr_scangle_it4.3364.5589
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.39→1.427 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.452 15
Rwork0.259 142
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)
10.1917-0.08470.03710.5871-0.10980.53920.0018-0.0258-0.0143-0.00320.010.0079-0.00710.0021-0.0118-0.0145-0.00180.0058-0.0051-0.0008-0.009133.14232.435810.9177
20.48960.048-0.06940.5292-0.09070.8093-0.010.02840.019-0.00360.0060.0060.02-0.00360.0039-0.0175-0.0006-0.0028-0.01050.0017-0.013533.18178.4131-14.4866
30.35670.09080.08850.69760.13610.5552-0.0117-0.02950.00710.00960.00750.0177-0.01490.02990.0042-0.012700.0045-0.0091-0.0024-0.01332.788127.56274.4837
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 711 - 71
2X-RAY DIFFRACTION2BB1 - 711 - 71
3X-RAY DIFFRACTION3CC1 - 741 - 74

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