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- PDB-6hvl: CdaA complex with c-di-AMP and AMP -

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Basic information

Entry
Database: PDB / ID: 6hvl
TitleCdaA complex with c-di-AMP and AMP
ComponentsDiadenylate cyclase
KeywordsTRANSFERASE / di-adenylate cyclase / second messenger / complex / c-di-AMP / AMP
Function / homology
Function and homology information


: / diadenylate cyclase activity / diadenylate cyclase / cAMP biosynthetic process / adenylate cyclase activity / ATP binding / plasma membrane
Similarity search - Function
YojJ-like (1 / DNA integrity scanning protein, DisA, N-terminal domain / Diadenylate cyclase CdaA, N-terminal domain / CdaA N-terminal transmembrane domain / Diadenylate cyclase CdaA / Diadenylate cyclase / 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. ...YojJ-like (1 / DNA integrity scanning protein, DisA, N-terminal domain / Diadenylate cyclase CdaA, N-terminal domain / CdaA N-terminal transmembrane domain / Diadenylate cyclase CdaA / Diadenylate cyclase / 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. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2BA / ADENOSINE MONOPHOSPHATE / : / PHOSPHATE ION / Diadenylate cyclase
Similarity search - Component
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHeidemann, J.L. / Neumann, P. / Ficner, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
Germany
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Crystal structures of the c-di-AMP-synthesizing enzyme CdaA.
Authors: Heidemann, J.L. / Neumann, P. / Dickmanns, A. / Ficner, R.
History
DepositionOct 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...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_struct_conn_angle / struct_conn
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 / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Diadenylate cyclase
B: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8986
Polymers38,7382
Non-polymers1,1604
Water1086
1
A: Diadenylate cyclase
hetero molecules

A: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3638
Polymers38,7382
Non-polymers1,6256
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_545y+1/3,x-1/3,-z+2/31
Buried area2470 Å2
ΔGint-46 kcal/mol
Surface area14500 Å2
MethodPISA
2
B: Diadenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7162
Polymers19,3691
Non-polymers3471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint1 kcal/mol
Surface area8020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.900, 121.900, 141.160
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Diadenylate cyclase / / DAC / Cyclic-di-AMP synthase / c-di-AMP synthase / Diadenylate cyclase CdaA


Mass: 19369.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria)
Strain: ATCC BAA-679 / EGD-e / Gene: dacA, cdaA, lmo2120 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8Y5E4, diadenylate cyclase

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Non-polymers , 5 types, 10 molecules

#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: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: PO4
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.61 Å3/Da / Density % sol: 52.79 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 m Ca(CH3OO)2, 0.1 M Na-HEPES pH 7.5, 10 % w/v PEG8000,

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.8→42.271 Å / Num. obs: 9435 / % possible obs: 93.1 % / Redundancy: 5.649 % / Biso Wilson estimate: 57.26 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.109 / Rrim(I) all: 0.118 / Χ2: 0.941 / Net I/σ(I): 12.39
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.8-2.95.6820.8051.939410.7260.87795.4
2.9-35.6730.5562.838360.8530.60595.4
3-3.15.5550.4923.227230.8680.53694.9
3.1-45.6250.1818.1836910.9880.19793.4
4-55.6670.06621.415870.9980.07293
5-65.6760.07420.157030.9980.08192
6-75.7010.06622.263540.9980.07190.3
7-85.8540.04428.921850.9990.04884.5
8-95.9830.03140.971180.9990.03388.7
9-105.6220.02746.05820.9990.0390.1
10-205.6010.02548.041880.9990.02786.2
20-304.850.02745.65200.9990.02980
30-505.40.01848.39510.0255.6
42.271-5030.0231.1720.02366.7

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4rv7

4rv7


Resolution: 2.8→42.271 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.51
RfactorNum. reflection% reflection
Rfree0.2337 495 5.25 %
Rwork0.1875 --
obs0.1899 9430 93.09 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 136.02 Å2 / Biso mean: 57.9376 Å2 / Biso min: 23.42 Å2
Refinement stepCycle: final / Resolution: 2.8→42.271 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2390 0 51 6 2447
Biso mean--63.81 43.74 -
Num. residues----312
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8003-3.08210.32731260.25242237236395
3.0821-3.52790.24581250.21862266239195
3.5279-4.4440.2121060.17362211231792
4.444-42.27550.21851380.16722221235990

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