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- PDB-1j74: Crystal Structure of Mms2 -

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Basic information

Entry
Database: PDB / ID: 1j74
TitleCrystal Structure of Mms2
ComponentsMMS2
KeywordsUNKNOWN FUNCTION / Mms2 / Uev / Ubiquitin / Ubc / DNA repair
Function / homology
Function and homology information


error-free postreplication DNA repair / UBC13-MMS2 complex / DNA double-strand break processing / positive regulation of protein K63-linked ubiquitination / postreplication repair / positive regulation of double-strand break repair / protein K63-linked ubiquitination / regulation of DNA repair / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint ...error-free postreplication DNA repair / UBC13-MMS2 complex / DNA double-strand break processing / positive regulation of protein K63-linked ubiquitination / postreplication repair / positive regulation of double-strand break repair / protein K63-linked ubiquitination / regulation of DNA repair / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / Formation of Incision Complex in GG-NER / protein polyubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / protein ubiquitination / extracellular exosome / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Roll / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-conjugating enzyme E2 variant 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMoraes, T.F. / Edwards, R.A. / McKenna, S. / Pastushok, L. / Xiao, W. / Glover, J.N.M. / Ellison, M.J.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Crystal structure of the human ubiquitin conjugating enzyme complex, hMms2-hUbc13.
Authors: Moraes, T.F. / Edwards, R.A. / McKenna, S. / Pastushok, L. / Xiao, W. / Glover, J.N. / Ellison, M.J.
History
DepositionMay 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MMS2


Theoretical massNumber of molelcules
Total (without water)16,3811
Polymers16,3811
Non-polymers00
Water1,78399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.190, 54.540, 108.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein MMS2


Mass: 16380.731 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q15819
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 1.9 Å3/Da / Density % sol: 35.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16% PEG 6000, 25mM NaCl, 100mM citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20-24 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
250 mMHEPES1drop
375 mM1dropNaCl
41 mMEDTA1drop
50.5 mMdithiothreitol1drop
616 %(w/v)PEG60001reservoir
725 mM1reservoirNaCl
8100 mMcitrate1reservoir

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 21, 2000 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 9995 / Num. obs: 9973 / % possible obs: 97.9 % / Redundancy: 5.35 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 4.5 / Net I/σ(I): 37.1
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3 % / Rmerge(I) obs: 0.129 / Mean I/σ(I) obs: 20 / Num. unique all: 445 / Rsym value: 12.9 / % possible all: 87.6
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 53554

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1J7D

1j7d


Resolution: 1.9→20 Å / Stereochemistry target values: CNS template
RfactorNum. reflection% reflectionSelection details
Rfree0.2459 472 -RANDOM
Rwork0.2134 ---
all-10194 --
obs-9972 97.8 %-
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1108 0 0 99 1207
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2649
X-RAY DIFFRACTIONc_bond_d0.004885
LS refinement shellResolution: 1.9→1.98 Å
RfactorNum. reflection
Rfree0.3271 50
Rwork0.2564 -
obs-986
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor obs: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS

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