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- PDB-3c21: Structure of a bacterial DNA damage sensor protein with reaction ... -

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Basic information

Entry
Database: PDB / ID: 3c21
TitleStructure of a bacterial DNA damage sensor protein with reaction product
ComponentsDNA integrity scanning protein disA
KeywordsDNA BINDING PROTEIN / DNA damage / DNA repair / DNA-binding
Function / homology
Function and homology information


diadenylate cyclase / diadenylate cyclase activity / adenylate cyclase activity / DNA repair / DNA binding / ATP binding
Similarity search - Function
DNA integrity scanning linker region / DNA integrity scanning, DisA, linker region / DNA integrity scanning protein, DisA / DisA, linker domain superfamily / DisA bacterial checkpoint controller linker region / YojJ-like (1 / DNA integrity scanning protein, DisA, N-terminal domain / Helix-hairpin-helix motif / : / DNA integrity scanning protein, DisA, N-terminal ...DNA integrity scanning linker region / DNA integrity scanning, DisA, linker region / DNA integrity scanning protein, DisA / DisA, linker domain superfamily / DisA bacterial checkpoint controller linker region / YojJ-like (1 / DNA integrity scanning protein, DisA, N-terminal domain / Helix-hairpin-helix motif / : / DNA integrity scanning protein, DisA, N-terminal / DNA integrity scanning protein, DisA, N-terminal domain superfamily / Helix-hairpin-helix motif / DisA bacterial checkpoint controller nucleotide-binding / Diadenylate cyclase (DAC) domain profile. / RuvA domain 2-like / Ferritin / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Up-down Bundle / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-2BA / DNA integrity scanning protein DisA
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWitte, G. / Hartung, S. / Buttner, K. / Hopfner, K.P.
CitationJournal: Mol.Cell / Year: 2008
Title: Structural Biochemistry of a Bacterial Checkpoint Protein Reveals Diadenylate Cyclase Activity Regulated by DNA Recombination Intermediates
Authors: Witte, G. / Hartung, S. / Buttner, K. / Hopfner, K.P.
History
DepositionJan 24, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Nov 1, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA integrity scanning protein disA
B: DNA integrity scanning protein disA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1863
Polymers85,5282
Non-polymers6581
Water1,874104
1
A: DNA integrity scanning protein disA
B: DNA integrity scanning protein disA
hetero molecules

A: DNA integrity scanning protein disA
B: DNA integrity scanning protein disA
hetero molecules

A: DNA integrity scanning protein disA
B: DNA integrity scanning protein disA
hetero molecules

A: DNA integrity scanning protein disA
B: DNA integrity scanning protein disA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)344,74612
Polymers342,1128
Non-polymers2,6344
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
2
A: DNA integrity scanning protein disA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4222
Polymers42,7641
Non-polymers6581
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: DNA integrity scanning protein disA


Theoretical massNumber of molelcules
Total (without water)42,7641
Polymers42,7641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.080, 109.080, 165.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein DNA integrity scanning protein disA


Mass: 42763.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9WY43
#2: Chemical ChemComp-2BA / (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide / bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate


Mass: 658.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N10O12P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.89 Å3/Da / Density % sol: 57.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Tris, 0.2M Ammoniumacetate, 35% MPD, 3mM ATP-gammaS, 3mM MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0099 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0099 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 27866 / Num. obs: 27866 / % possible obs: 98.2 % / Redundancy: 9.63 % / Rmerge(I) obs: 0.075 / Rsym value: 0.079 / Net I/σ(I): 24.51
Reflection shellResolution: 2.7→2.86 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 7.19 / Num. unique all: 4315 / Rsym value: 0.379 / % possible all: 96.6

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.004data extraction
MAR345data collection
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3C1Y

3c1y


Resolution: 2.7→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.269 2762 9.8 %RANDOM
Rwork0.208 ---
obs-27823 98.6 %-
Solvent computationBsol: 42.491 Å2
Displacement parametersBiso mean: 42.631 Å2
Baniso -1Baniso -2Baniso -3
1-4.13 Å20 Å20 Å2
2--4.13 Å20 Å2
3----8.26 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5594 0 44 104 5742
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.12
X-RAY DIFFRACTIONc_mcbond_it1.3121.5
X-RAY DIFFRACTIONc_scbond_it2.1652
X-RAY DIFFRACTIONc_mcangle_it2.232
X-RAY DIFFRACTIONc_scangle_it3.4062.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5ligand.paramligand.top

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