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- PDB-1ay9: WILD-TYPE UMUD' FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 1ay9
TitleWILD-TYPE UMUD' FROM E. COLI
ComponentsUMUD PROTEIN
KeywordsMUTAGENESIS PROTEIN / DNA REPAIR / HYDROLASE
Function / homology
Function and homology information


DNA polymerase V complex / SOS response / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / translesion synthesis / ATP-dependent activity, acting on DNA / serine-type peptidase activity / single-stranded DNA binding / nucleic acid binding / DNA-directed DNA polymerase activity / DNA repair ...DNA polymerase V complex / SOS response / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / translesion synthesis / ATP-dependent activity, acting on DNA / serine-type peptidase activity / single-stranded DNA binding / nucleic acid binding / DNA-directed DNA polymerase activity / DNA repair / DNA damage response / regulation of DNA-templated transcription / proteolysis / DNA binding / identical protein binding / cytosol
Similarity search - Function
Peptidase S24, LexA-like / Umud Fragment, subunit A / Umud Fragment, subunit A / : / LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Protein UmuD / Protein UmuD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPeat, T.S. / Frank, E.G. / Mcdonald, J.P. / Levine, A.S. / Woodgate, R. / Hendrickson, W.A.
Citation
Journal: Structure / Year: 1996
Title: The UmuD' protein filament and its potential role in damage induced mutagenesis.
Authors: Peat, T.S. / Frank, E.G. / McDonald, J.P. / Levine, A.S. / Woodgate, R. / Hendrickson, W.A.
#1: Journal: Nature / Year: 1996
Title: Structure of the UmuD' Protein and its Regulation in Response to DNA Damage
Authors: Peat, T.S. / Frank, E.G. / Mcdonald, J.P. / Levine, A.S. / Woodgate, R. / Hendrickson, W.A.
History
DepositionNov 15, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UMUD PROTEIN
B: UMUD PROTEIN


Theoretical massNumber of molelcules
Total (without water)23,3352
Polymers23,3352
Non-polymers00
Water64936
1
A: UMUD PROTEIN
B: UMUD PROTEIN

A: UMUD PROTEIN
B: UMUD PROTEIN


Theoretical massNumber of molelcules
Total (without water)46,6694
Polymers46,6694
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_454y-1/2,-x+1/2,z-1/41
MethodPQS
2
A: UMUD PROTEIN

B: UMUD PROTEIN


Theoretical massNumber of molelcules
Total (without water)23,3352
Polymers23,3352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_454y-1/2,-x+1/2,z-1/41
Buried area2260 Å2
ΔGint-22 kcal/mol
Surface area11790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.100, 53.100, 164.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.341469, 0.939004, -0.040869), (0.939459, -0.34231, -0.015534), (-0.028576, -0.033091, -0.999044)
Vector: -22.09, 36.09, 124.011)

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Components

#1: Protein UMUD PROTEIN


Mass: 11667.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
References: UniProt: P04153, UniProt: P0AG11*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.48 Å3/Da / Density % sol: 47 %
Crystal growpH: 6 / Details: 100MM CACODYLATE BUFFER PH 6.0
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMcacodylate1reservoir
2600 mM1reservoirLi2SO4
320 mM1reservoirMgCl2
45 mMdithiothreitol1reservoir
52 mg/mlfree DL-methionine1reservoir
612-15 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Dec 1, 1990
RadiationMonochromator: SINGLE CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 3→15 Å / Num. obs: 4912 / % possible obs: 90 % / Observed criterion σ(I): 2 / Redundancy: 3.2 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
CCP4data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UMU

1umu


Resolution: 3→15 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.287 217 6 %RANDOM
Rwork0.218 ---
obs0.218 4912 90 %-
Displacement parametersBiso mean: 10.7 Å2
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1592 0 0 36 1628
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.62
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 3→3.11 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.324 24 6 %
Rwork0.253 417 -
obs--89 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
X-RAY DIFFRACTION3
X-RAY DIFFRACTION4

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