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- PDB-4yvz: Structure of Thermotoga maritima DisA in complex with 3'-dATP/Mn2+ -

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Basic information

Entry
Database: PDB / ID: 4yvz
TitleStructure of Thermotoga maritima DisA in complex with 3'-dATP/Mn2+
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 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
3'-DEOXYADENOSINE-5'-TRIPHOSPHATE / : / DNA integrity scanning protein DisA
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.495 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 20, 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 / Data collection / Category: diffrn_source / pdbx_audit_support
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)86,7308
Polymers85,5282
Non-polymers1,2026
Water2,000111
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)346,92032
Polymers342,1128
Non-polymers4,80824
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 area37280 Å2
ΔGint-129 kcal/mol
Surface area111110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.490, 107.490, 168.790
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-3AT / 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE / CORDYCEPIN TRIPHOSPHATE / Deoxyadenosine triphosphate


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 56.85 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop
Details: 30% (v/v) MPD, 200 mM ammoniumacetate, 100 mM Tris-HCl
PH range: 8.0-8.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.23953 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23953 Å / Relative weight: 1
ReflectionResolution: 2.495→168.8 Å / Num. obs: 65492 / % possible obs: 99.6 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 15.9
Reflection shellResolution: 2.495→2.56 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.052 / Mean I/σ(I) obs: 2.8 / % possible all: 94.5

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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: 2.495→168.79 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2189 3255 4.97 %
Rwork0.1642 --
obs0.167 65492 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.495→168.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5594 0 64 111 5769
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085739
X-RAY DIFFRACTIONf_angle_d1.1037769
X-RAY DIFFRACTIONf_dihedral_angle_d15.9812199
X-RAY DIFFRACTIONf_chiral_restr0.044917
X-RAY DIFFRACTIONf_plane_restr0.004978
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4953-2.53260.33391270.2882464X-RAY DIFFRACTION91
2.5326-2.57220.30861400.24682710X-RAY DIFFRACTION100
2.5722-2.61430.29531430.2422702X-RAY DIFFRACTION100
2.6143-2.65940.29161390.22852718X-RAY DIFFRACTION100
2.6594-2.70780.29521430.23052722X-RAY DIFFRACTION100
2.7078-2.75990.30911430.22192726X-RAY DIFFRACTION100
2.7599-2.81620.30081360.2212713X-RAY DIFFRACTION100
2.8162-2.87750.31021380.20592718X-RAY DIFFRACTION100
2.8775-2.94440.28691440.20372701X-RAY DIFFRACTION100
2.9444-3.0180.26071470.19282710X-RAY DIFFRACTION100
3.018-3.09960.31051400.20542726X-RAY DIFFRACTION100
3.0996-3.19090.26891440.19112721X-RAY DIFFRACTION100
3.1909-3.29390.2261430.18312725X-RAY DIFFRACTION100
3.2939-3.41160.25461450.17452691X-RAY DIFFRACTION100
3.4116-3.54820.23121410.15722748X-RAY DIFFRACTION100
3.5482-3.70970.20271440.14992717X-RAY DIFFRACTION100
3.7097-3.90530.20271480.13992695X-RAY DIFFRACTION100
3.9053-4.150.15891430.1322719X-RAY DIFFRACTION100
4.15-4.47040.14661410.12092739X-RAY DIFFRACTION100
4.4704-4.92030.15381430.12532701X-RAY DIFFRACTION100
4.9203-5.63240.22791430.15372713X-RAY DIFFRACTION100
5.6324-7.09620.21811400.17872717X-RAY DIFFRACTION100
7.0962-169.17740.16761400.12452741X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 13.1059 Å / Origin y: -36.6604 Å / Origin z: 43.8695 Å
111213212223313233
T0.4052 Å2-0.0764 Å2-0.0125 Å2-0.3924 Å20.0089 Å2--0.4765 Å2
L0.1055 °2-0.0167 °2-0.0412 °2-0.1074 °2-0.0761 °2--1.9188 °2
S-0.017 Å °-0.0226 Å °0.0412 Å °0.0125 Å °-0.0377 Å °-0.0331 Å °-0.23 Å °0.2335 Å °0.0001 Å °
Refinement TLS groupSelection details: all

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