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- PDB-1umu: STRUCTURE DETERMINATION OF UMUD' BY MAD PHASING OF THE SELENOMETH... -

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Basic information

Entry
Database: PDB / ID: 1umu
TitleSTRUCTURE DETERMINATION OF UMUD' BY MAD PHASING OF THE SELENOMETHIONYL PROTEIN
ComponentsUMUD'
KeywordsSOS MUTAGENESIS / INDUCED MUTAGENESIS / DNA REPAIR / BETA-LACTAMASE CLEAVAGE REACTION / LEXA REPRESSOR / LAMBDA CI
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 / MAD METHOD / Resolution: 2.5 Å
AuthorsPeat, T.S. / Hendrickson, W.A.
Citation
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.
#1: Journal: To be Published
Title: Production and Crystallization of a Selenomethionyl Variant of UmuD', an Escherichia Coli SOS Response Protein
Authors: Peat, T.S. / Frank, E.G. / Woodgate, R. / Hendrickson, W.A.
History
DepositionMar 7, 1996Processing site: BNL
Revision 1.0Aug 1, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UMUD'
B: UMUD'


Theoretical massNumber of molelcules
Total (without water)24,8592
Polymers24,8592
Non-polymers00
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.800, 52.800, 160.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein UMUD'


Mass: 12429.735 Da / Num. of mol.: 2 / Fragment: UMUD', RESIDUES 25 - 139
Mutation: DEL(1-24), M138T, M61 AND M110 SUBSTITUTED BY SELENOMETHIONINE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Description: T7 PROMOTER / Plasmid: PALTER
Gene (production host): UMUD, WITH THE FIRST 24 AMINO ACID CODONS REMOVED
Production host: 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.: 77 / Source method: isolated from a natural source / Formula: H2O
Compound detailsUMUD GOES THROUGH A SELF CLEAVAGE REACTION TO FORM THE MUTAGENETICALLY ACTIVE FORM OF THE PROTEIN ...UMUD GOES THROUGH A SELF CLEAVAGE REACTION TO FORM THE MUTAGENETICALLY ACTIVE FORM OF THE PROTEIN UMUD'. UMUD'S CLEAVAGE MECHANISM IS SIMILAR TO THE BETA-LACTAMASE REACTION. THERE IS HOMOLOGY TO C-TERMINAL PORTIONS OF LAMBDA CI, AND E. COLI LEXA REPRESSOR PROTEINS.
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 47 %
Description: THE COMPLETENESS GIVEN ABOVE IS CALCULATED NOT SEPARATING THE BIJVOETS.
Crystal growpH: 5.8
Details: THE CRYSTALS WERE GROWN FROM 600MM LISO4, 20MM MGCL2, 100MM CACODYLATE BUFFER PH 5.8, 5MM DTT AT 20C WITH A PROTEIN CONCENTRATION OF 12-15 MG/ML. THE CRYSTALS WERE FROZEN AT 100K IN PARATONE ...Details: THE CRYSTALS WERE GROWN FROM 600MM LISO4, 20MM MGCL2, 100MM CACODYLATE BUFFER PH 5.8, 5MM DTT AT 20C WITH A PROTEIN CONCENTRATION OF 12-15 MG/ML. THE CRYSTALS WERE FROZEN AT 100K IN PARATONE FOR DATA COLLECTION AT THE NSLS X4A BEAMLINE.
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMcacodylate1reservoir
2600 mM1reservoirLi2SO4
320 mM1reservoirMgCl2
45 mMDTT1reservoir
52 mg/mlfree DL-methionine1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A
Wavelength: 0.9871, 0.9794, 0.9792, 0.9686; 0.9793, 0.9791, 0.9686
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Aug 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98711
20.97941
30.97921
40.96861
50.97931
60.97911
ReflectionResolution: 3→20 Å / Num. obs: 7500 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 2
Reflection shellResolution: 3→3.1 Å

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Processing

Software
NameVersionClassification
MADSYSphasing
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
CCP4MODIFIED LOCALLYdata scaling
X-PLORphasing
RefinementMethod to determine structure: MAD METHOD / Resolution: 2.5→6 Å / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflection
Rfree0.303 -6 %
Rwork0.207 --
obs0.207 7016 98.9 %
Displacement parametersBiso mean: 24.2 Å2
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2129 0 0 77 2206
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.8
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

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