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- PDB-5emz: Crystal structure of K48-linked diubiquitin with F45W mutation in... -

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Basic information

Entry
Database: PDB / ID: 5emz
TitleCrystal structure of K48-linked diubiquitin with F45W mutation in the proximal unit
Components(Polyubiquitin-B) x 2
KeywordsSIGNALING PROTEIN / ubiquitin signaling / multidomain system / fluorescence assay
Function / homologysymbiont entry into host cell via disruption of host cell glycocalyx / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / symbiont entry into host cell via disruption of host cell envelope / virus tail / Pectin lyase fold / Pectin lyase fold/virulence factor / Ubiquitin family / Tail fiber
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsNakasone, M.A. / Paukstelis, P.J. / Fushman, D.
CitationJournal: To Be Published
Title: Structural characterization and practical fluorescence applications of the F45W ubiquitin mutant
Authors: Nakasone, M.A. / Geng, C. / Chojnacki, M. / Glickman, M. / Paukstelis, P.J. / Fushman, D.
History
DepositionNov 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Polyubiquitin-B
B: Polyubiquitin-B
C: Polyubiquitin-B
D: Polyubiquitin-B
E: Polyubiquitin-B
F: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,04610
Polymers51,6626
Non-polymers3844
Water10,106561
1
A: Polyubiquitin-B
B: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3173
Polymers17,2212
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-24 kcal/mol
Surface area7610 Å2
MethodPISA
2
C: Polyubiquitin-B
D: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3173
Polymers17,2212
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-24 kcal/mol
Surface area7620 Å2
MethodPISA
3
E: Polyubiquitin-B
F: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4134
Polymers17,2212
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-25 kcal/mol
Surface area7860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.870, 78.920, 91.510
Angle α, β, γ (deg.)90.00, 97.93, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-281-

HOH

21E-278-

HOH

31E-287-

HOH

41E-300-

HOH

51E-301-

HOH

61F-192-

HOH

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Components

#1: Protein Polyubiquitin-B


Mass: 8604.845 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#2: Protein Polyubiquitin-B


Mass: 8615.867 Da / Num. of mol.: 3 / Mutation: F45W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: LiSO Tris PEG-3350 / PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.66→43.68 Å / Num. all: 85363 / Num. obs: 46959 / % possible obs: 95.84 % / Redundancy: 1.8 % / Net I/σ(I): 7.94

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata scaling
PHASERphasing
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M3J

3m3j


Resolution: 1.66→43.676 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 20.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2089 2332 4.97 %
Rwork0.171 --
obs0.1729 46956 95.83 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.66→43.676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3520 0 20 561 4101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063652
X-RAY DIFFRACTIONf_angle_d0.9234956
X-RAY DIFFRACTIONf_dihedral_angle_d14.1281428
X-RAY DIFFRACTIONf_chiral_restr0.032601
X-RAY DIFFRACTIONf_plane_restr0.004634
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.69390.3073700.27772145X-RAY DIFFRACTION76
1.6939-1.73070.29641200.25932485X-RAY DIFFRACTION91
1.7307-1.7710.25651570.24312580X-RAY DIFFRACTION96
1.771-1.81530.27931420.22942637X-RAY DIFFRACTION97
1.8153-1.86440.30061560.20872602X-RAY DIFFRACTION96
1.8644-1.91920.24031460.19582635X-RAY DIFFRACTION97
1.9192-1.98120.2271470.18552650X-RAY DIFFRACTION97
1.9812-2.0520.24011250.18482673X-RAY DIFFRACTION97
2.052-2.13410.21731590.17632626X-RAY DIFFRACTION97
2.1341-2.23130.21571310.17322659X-RAY DIFFRACTION97
2.2313-2.34890.23411410.1732687X-RAY DIFFRACTION98
2.3489-2.49610.20361400.17422661X-RAY DIFFRACTION98
2.4961-2.68870.24241480.17562683X-RAY DIFFRACTION98
2.6887-2.95930.21941400.16992677X-RAY DIFFRACTION98
2.9593-3.38730.18661330.15882715X-RAY DIFFRACTION99
3.3873-4.26710.17311360.13452732X-RAY DIFFRACTION99
4.2671-43.69120.14831410.14452777X-RAY DIFFRACTION99

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