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- PDB-3c1y: Structure of bacterial DNA damage sensor protein with co-purified... -

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Basic information

Entry
Database: PDB / ID: 3c1y
TitleStructure of bacterial DNA damage sensor protein with co-purified and co-crystallized ligand
ComponentsDNA integrity scanning protein disA
KeywordsDNA BINDING PROTEIN / DNA damage / DNA repair / DNA-binding
Function / homology
Function and homology information


diadenylate cyclase activity / diadenylate cyclase / : / 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 protein, DisA, N-terminal domain superfamily ...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 / DisA bacterial checkpoint controller nucleotide-binding / Diadenylate cyclase (DAC) domain profile. / Helix-hairpin-helix motif / 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 / MAD / Resolution: 2.1 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 1.3Mar 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / 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
Water3,909217
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_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+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)108.329, 108.329, 166.415
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 / Water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Tris pH 7.5, 0.2M Ammoniumacetate, 35% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06SA11
SYNCHROTRONESRF ID2920.97639, 0.97686
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDAug 9, 2006
ADSC QUANTUM 3152CCDJul 22, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.976391
30.976861
ReflectionResolution: 2.1→20 Å / Num. all: 58493 / Num. obs: 58168 / % possible obs: 99.6 % / Redundancy: 4.25 % / Rmerge(I) obs: 0.094 / Rsym value: 0.082 / Net I/σ(I): 13.07
Reflection shellResolution: 2.1→2.3 Å / Redundancy: 4.25 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 3.63 / Num. unique all: 26289 / Rsym value: 0.515 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.004data extraction
MAR345data collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2944 5 %RANDOM
Rwork0.223 ---
obs-58117 99.5 %-
Solvent computationBsol: 46.303 Å2
Displacement parametersBiso mean: 38.184 Å2
Baniso -1Baniso -2Baniso -3
1-5.927 Å20 Å20 Å2
2--5.927 Å20 Å2
3----11.854 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5594 0 44 217 5855
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.06
X-RAY DIFFRACTIONc_mcbond_it1.3611.5
X-RAY DIFFRACTIONc_scbond_it2.3572
X-RAY DIFFRACTIONc_mcangle_it2.1292
X-RAY DIFFRACTIONc_scangle_it3.592.5
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 DIFFRACTION55ap.param5ap.top

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