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- PDB-4rle: Crystal structure of the c-di-AMP binding PII-like protein DarA -

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Basic information

Entry
Database: PDB / ID: 4rle
TitleCrystal structure of the c-di-AMP binding PII-like protein DarA
ComponentsUncharacterized protein YaaQ
KeywordsUNKNOWN FUNCTION / PII-like / cdiAMP
Function / homology
Function and homology information


Cyclic-di-AMP receptor / Cyclic-di-AMP receptor / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2BA / NICKEL (II) ION / Cyclic di-AMP receptor A
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsDickmanns, A. / Neumann, P. / Ficner, R.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Identification, Characterization, and Structure Analysis of the Cyclic di-AMP-binding PII-like Signal Transduction Protein DarA.
Authors: Gundlach, J. / Dickmanns, A. / Schroder-Tittmann, K. / Neumann, P. / Kaesler, J. / Kampf, J. / Herzberg, C. / Hammer, E. / Schwede, F. / Kaever, V. / Tittmann, K. / Stulke, J. / Ficner, R.
History
DepositionOct 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Feb 11, 2015Group: Database references
Revision 1.3Sep 4, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rsym_value
Revision 1.4Sep 20, 2023Group: 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 / 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: Uncharacterized protein YaaQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6703
Polymers12,9531
Non-polymers7172
Water2,612145
1
A: Uncharacterized protein YaaQ
hetero molecules

A: Uncharacterized protein YaaQ
hetero molecules

A: Uncharacterized protein YaaQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0109
Polymers38,8583
Non-polymers2,1516
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area7810 Å2
ΔGint-77 kcal/mol
Surface area17710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.521, 56.521, 58.201
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-202-

NI

21A-354-

HOH

31A-369-

HOH

41A-405-

HOH

51A-419-

HOH

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Components

#1: Protein Uncharacterized protein YaaQ / DarA


Mass: 12952.741 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: BSU00290, yaaQ / Plasmid: pWH844 / Production host: Escherichia coli (E. coli) / References: UniProt: P37538
#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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.07 Å3/Da / Density % sol: 40.63 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.1-0.2 M sodium tartrate, 16-20% PEG5000, 10 mM DTT, vapor diffusion, sitting drop, temperature 292K
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.91 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 12, 2014 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.3→37.461 Å / Num. all: 26017 / Num. obs: 26017 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 14.05 Å2 / Rmerge(I) obs: 0.025 / Χ2: 0.977 / Net I/σ(I): 38.86
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.3-1.350.17610.49176322789100
1.35-1.40.12614.25151112377100
1.4-1.50.09218.38238463875100
1.5-2.660.02746.119387113886100
2.66-3.240.0275.519256137799.6
3.24-3.820.0274.23767656100
3.82-4.40.02283.5248636099.7
4.4-140.02577.44478667599.7
14-170.01870.9246888.9
170.01655.61521493.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
DNAdata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3M05

3m05


Resolution: 1.3→37.461 Å / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 1.38 / σ(I): 0 / Phase error: 15.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1545 911 3.5 %RANDOM
Rwork0.1296 ---
obs0.1305 26015 99.93 %-
all-26017 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 326.4 Å2 / Biso mean: 37.0171 Å2 / Biso min: 9.17 Å2
Refine analyzeLuzzati coordinate error obs: 0.07 Å
Refinement stepCycle: LAST / Resolution: 1.3→37.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms901 0 45 145 1091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091092
X-RAY DIFFRACTIONf_angle_d1.4691500
X-RAY DIFFRACTIONf_chiral_restr0.054168
X-RAY DIFFRACTIONf_plane_restr0.008192
X-RAY DIFFRACTIONf_dihedral_angle_d18.624454
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.3-1.36860.17391300.116735753705
1.3686-1.45430.15981290.108835643693
1.4543-1.56660.15311290.101735733702
1.5666-1.72420.15861310.10336013732
1.7242-1.97370.14161290.113635643693
1.9737-2.48660.1441310.141735893720
2.4866-37.47680.16041320.140636383770
Refinement TLS params.Method: refined / Origin x: -0.963 Å / Origin y: 5.402 Å / Origin z: 108.046 Å
111213212223313233
T1.0871 Å20.4224 Å2-0.2868 Å2-0.3752 Å2-0.0763 Å2--1.3349 Å2
L3.1175 °2-0.04 °24.5085 °2-1.7071 °22.0682 °2--9.6702 °2
S-1.9985 Å °3.4292 Å °1.2309 Å °-0.9388 Å °1.0337 Å °-1.4214 Å °-2.6943 Å °2.1038 Å °-2.1361 Å °
Refinement TLS groupSelection details: ( CHAIN A AND RESID 74:88 )

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