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- PDB-8ic9: Lys48-linked K48C-diubiquitin -

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Basic information

Entry
Database: PDB / ID: 8ic9
TitleLys48-linked K48C-diubiquitin
Components
  • Polyubiquitin-B
  • Ubiquitin
KeywordsSIGNALING PROTEIN / UBIQUITIN / ISOPEPTIDE BOND
Function / homology
Function and homology information


symbiont entry into host cell via disruption of host cell glycocalyx / symbiont entry into host cell via disruption of host cell envelope / virus tail
Similarity search - Function
Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Pectin lyase fold / Pectin lyase fold/virulence factor / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsHiranyakorn, M. / Yagi-Utsumi, M. / Yanaka, S. / Ohtsuka, N. / Momiyama, N. / Satoh, T. / Kato, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP18H05229 Japan
Japan Science and TechnologyJPMJPR22AC Japan
CitationJournal: Int J Mol Sci / Year: 2023
Title: Mutational and Environmental Effects on the Dynamic Conformational Distributions of Lys48-Linked Ubiquitin Chains.
Authors: Hiranyakorn, M. / Yagi-Utsumi, M. / Yanaka, S. / Ohtsuka, N. / Momiyama, N. / Satoh, T. / Kato, K.
History
DepositionFeb 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyubiquitin-B
B: Ubiquitin
C: Polyubiquitin-B
D: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)34,2554
Polymers34,2554
Non-polymers00
Water3,135174
1
A: Polyubiquitin-B
B: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)17,1282
Polymers17,1282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-7 kcal/mol
Surface area7750 Å2
MethodPISA
2
C: Polyubiquitin-B
D: Ubiquitin


Theoretical massNumber of molelcules
Total (without water)17,1282
Polymers17,1282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-6 kcal/mol
Surface area7720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.790, 31.191, 25.272
Angle α, β, γ (deg.)90.000, 106.929, 88.650
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Polyubiquitin-B


Mass: 8550.794 Da / Num. of mol.: 2 / Mutation: K48C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Plasmid: PT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0CG47
#2: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Plasmid: pT7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0CG47
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 1.91 Å3/Da / Density % sol: 35.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 38% 2-methyl-2,4-pentanediol and 50 mM sodium citrate (pH 4.0)
PH range: 4.0-4.5

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 19, 2021
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.25→19.641 Å / Num. obs: 66682 / % possible obs: 95.1 % / Redundancy: 3.6 % / CC1/2: 0.992 / Rmerge(I) obs: 0.062 / Net I/σ(I): 6.7
Reflection shellResolution: 1.25→1.27 Å / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 11849 / CC1/2: 0.911 / % possible all: 93.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→19.641 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.978 / WRfactor Rfree: 0.267 / WRfactor Rwork: 0.222 / SU B: 2.28 / SU ML: 0.041 / Average fsc free: 0.9412 / Average fsc work: 0.9488 / Cross valid method: FREE R-VALUE / ESU R: 0.061 / ESU R Free: 0.057
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2188 3360 5.039 %
Rwork0.1861 63320 -
all0.188 --
obs-66680 95.071 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.291 Å2
Baniso -1Baniso -2Baniso -3
1--1.427 Å20.758 Å2-0.568 Å2
2--1.236 Å20.399 Å2
3---0.491 Å2
Refinement stepCycle: LAST / Resolution: 1.25→19.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2400 0 0 174 2574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132440
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152468
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.6573282
X-RAY DIFFRACTIONr_angle_other_deg1.3961.5915710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1755304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.01923.548124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33615498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0181516
X-RAY DIFFRACTIONr_chiral_restr0.0790.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022702
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02498
X-RAY DIFFRACTIONr_nbd_refined0.2120.2357
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.22266
X-RAY DIFFRACTIONr_nbtor_refined0.160.21145
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21230
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2133
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0380.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2330.228
X-RAY DIFFRACTIONr_nbd_other0.2170.286
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1870.230
X-RAY DIFFRACTIONr_mcbond_it3.8361.9631216
X-RAY DIFFRACTIONr_mcbond_other3.8241.9571214
X-RAY DIFFRACTIONr_mcangle_it4.6072.931514
X-RAY DIFFRACTIONr_mcangle_other4.5912.931514
X-RAY DIFFRACTIONr_scbond_it3.9582.4661224
X-RAY DIFFRACTIONr_scbond_other3.9592.4661224
X-RAY DIFFRACTIONr_scangle_it4.6313.4791766
X-RAY DIFFRACTIONr_scangle_other4.6293.4791766
X-RAY DIFFRACTIONr_lrange_it5.08723.3412465
X-RAY DIFFRACTIONr_lrange_other5.08823.3352463
X-RAY DIFFRACTIONr_rigid_bond_restr3.19634908
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.2820.3722880.3924487X-RAY DIFFRACTION93.2253
1.282-1.3170.3572500.3574478X-RAY DIFFRACTION93.1259
1.317-1.3550.3432470.3444357X-RAY DIFFRACTION93.806
1.355-1.3970.3862160.3144230X-RAY DIFFRACTION94.1351
1.397-1.4420.3122120.3044110X-RAY DIFFRACTION93.7527
1.442-1.4930.2831970.2624104X-RAY DIFFRACTION94.6106
1.493-1.5490.2751680.2213864X-RAY DIFFRACTION94.4262
1.549-1.6120.2441970.2123734X-RAY DIFFRACTION94.4498
1.612-1.6830.2441960.1963614X-RAY DIFFRACTION95.3931
1.683-1.7640.2321990.1623382X-RAY DIFFRACTION95.1887
1.764-1.8590.2161990.1543276X-RAY DIFFRACTION96.1007
1.859-1.9710.241620.1263169X-RAY DIFFRACTION96.4948
1.971-2.1050.1711370.1393006X-RAY DIFFRACTION96.8269
2.105-2.2720.1751450.1422722X-RAY DIFFRACTION96.8581
2.272-2.4860.1941460.1482553X-RAY DIFFRACTION97.2613
2.486-2.7740.2231120.1612312X-RAY DIFFRACTION97.2713
2.774-3.1920.228940.1562064X-RAY DIFFRACTION97.4266
3.192-3.8850.175920.1721727X-RAY DIFFRACTION97.4812
3.885-5.3940.167370.1671397X-RAY DIFFRACTION97.551
5.394-19.6410.172660.258734X-RAY DIFFRACTION93.5673

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