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- PDB-4yxj: Structure of Thermotoga maritima DisA in complex with ApCpp -

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Basic information

Entry
Database: PDB / ID: 4yxj
TitleStructure of Thermotoga maritima DisA in complex with ApCpp
ComponentsDNA integrity scanning protein DisA
KeywordsDNA BINDING PROTEIN / c-di-AMP synthesis / DAC domain / Inhibitor / pre-reaction state / transferase
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
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / DNA integrity scanning protein DisA
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsMueller, M. / Deimling, T. / Hopfner, K.-P. / Witte, G.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation3717/2-1 Germany
German Research FoundationGRK1721 Germany
CitationJournal: Biochem.J. / Year: 2015
Title: Structural analysis of the diadenylate cyclase reaction of DNA-integrity scanning protein A (DisA) and its inhibition by 3'-dATP.
Authors: Muller, M. / Deimling, T. / Hopfner, K.P. / Witte, G.
History
DepositionMar 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Aug 5, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 10, 2024Group: 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: DNA integrity scanning protein DisA
B: DNA integrity scanning protein DisA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,5384
Polymers85,5282
Non-polymers1,0102
Water3,351186
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)346,15416
Polymers342,1128
Non-polymers4,0428
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
Buried area34290 Å2
ΔGint5 kcal/mol
Surface area112490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.250, 108.250, 166.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein DNA integrity scanning protein DisA / Cyclic di-AMP synthase / c-di-AMP synthase / Diadenylate cyclase


Mass: 42763.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: disA, TM_0200 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q9WY43, diadenylate cyclase
#2: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.84 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 30% (v/v) MPD, 200mM Ammonium acetate, 100 mM TRis-HCl
PH range: 7-8.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00149 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00149 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 32830 / % possible obs: 99.2 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 15.5
Reflection shellResolution: 2.55→2.61 Å / Redundancy: 3 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 2.1 / % possible all: 93.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3c1z

3c1z


Resolution: 2.55→48.411 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 26.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2433 1578 4.81 %
Rwork0.1899 --
obs0.1926 32808 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→48.411 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5592 0 62 186 5840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095732
X-RAY DIFFRACTIONf_angle_d1.1257760
X-RAY DIFFRACTIONf_dihedral_angle_d16.5192220
X-RAY DIFFRACTIONf_chiral_restr0.043918
X-RAY DIFFRACTIONf_plane_restr0.004976
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5481-2.63030.34531330.26742665X-RAY DIFFRACTION95
2.6303-2.72430.31911380.25932795X-RAY DIFFRACTION99
2.7243-2.83340.33581540.26112789X-RAY DIFFRACTION100
2.8334-2.96230.32631370.23082797X-RAY DIFFRACTION100
2.9623-3.11850.26331250.22412847X-RAY DIFFRACTION100
3.1185-3.31380.27171410.21282836X-RAY DIFFRACTION100
3.3138-3.56960.28131460.1942816X-RAY DIFFRACTION100
3.5696-3.92870.22371400.16782861X-RAY DIFFRACTION100
3.9287-4.49680.17671620.14982863X-RAY DIFFRACTION99
4.4968-5.66410.21231620.16052898X-RAY DIFFRACTION100
5.6641-48.41960.22371400.17763063X-RAY DIFFRACTION99

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