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- PDB-7a7e: Structure of a delta-N mutant - E232start - of PA1120 (TpbB or Yf... -

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Basic information

Entry
Database: PDB / ID: 7a7e
TitleStructure of a delta-N mutant - E232start - of PA1120 (TpbB or YfiN) from Pseudomonas aeruginosa (PAO1) comprising only the GGDEF domain
ComponentsDiguanylate cyclase TpbB
KeywordsLIGASE / c-di-GMP / GTP / diguanylate cyclase / biofilm
Function / homology
Function and homology information


diguanylate cyclase / diguanylate cyclase activity / GTP binding / signal transduction / metal ion binding / plasma membrane
Similarity search - Function
Periplasmic sensor domain CHASE8 / Periplasmic sensor domain / : / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / GGDEF domain profile. / GGDEF domain ...Periplasmic sensor domain CHASE8 / Periplasmic sensor domain / : / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / GGDEF domain profile. / GGDEF domain / HAMP domain / Nucleotide cyclase / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
Diguanylate cyclase TpbB
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsGiardina, G. / Rinaldo, S. / Mantoni, F. / Brunotti, P.
Funding support Italy, 1items
OrganizationGrant numberCountry
Italian Ministry of EducationRBFR10LHD1 Italy
CitationJournal: Life / Year: 2021
Title: Studying GGDEF Domain in the Act: Minimize Conformational Frustration to Prevent Artefacts.
Authors: Mantoni, F. / Scribani Rossi, C. / Paiardini, A. / Di Matteo, A. / Cappellacci, L. / Petrelli, R. / Ricciutelli, M. / Paone, A. / Cutruzzola, F. / Giardina, G. / Rinaldo, S.
History
DepositionAug 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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

Downloads & links

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Assembly

Deposited unit
A: Diguanylate cyclase TpbB
B: Diguanylate cyclase TpbB
C: Diguanylate cyclase TpbB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7516
Polymers67,6783
Non-polymers733
Water1267
1
A: Diguanylate cyclase TpbB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5842
Polymers22,5591
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Diguanylate cyclase TpbB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5842
Polymers22,5591
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Diguanylate cyclase TpbB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5842
Polymers22,5591
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.642, 85.104, 126.975
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Diguanylate cyclase TpbB


Mass: 22559.320 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: DeltaN Mutant (E232start) missing the first 232 N-terminal residues
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: tpbB, PA1120 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9I4L5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.18 Å3/Da / Density % sol: 61.31 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein concentration: 2.5 mg/ml Protein Buffer: Buffer 250mM NaCl 10mM Tris pH 8 2% Gly, 5mM MgCl2 Precipitant: 0.2 M Ammonio Acetate, 0.1M Tri Sodium Citrate pH 5.5, 30% w/v PEG 4K Cryo: +20% GLY

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91801 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91801 Å / Relative weight: 1
ReflectionResolution: 2.8→49.64 Å / Num. obs: 21951 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.996 / Rmerge(I) obs: 0.255 / Rpim(I) all: 0.072 / Rrim(I) all: 0.265 / Net I/σ(I): 10.5 / Num. measured all: 290324
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.8-2.9513.51.7034293131750.6820.4781.771.7100
8.85-49.6411.10.036871778210.0110.03848.499.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.609
Highest resolutionLowest resolution
Rotation42.88 Å3.23 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.2.7data scaling
MOLREP11.2.05phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IOB

4iob


Resolution: 2.8→49 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.1795 / WRfactor Rwork: 0.1786 / FOM work R set: 0.7413 / SU R Cruickshank DPI: 0.587 / SU Rfree: 0.2852 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.587 / ESU R Free: 0.285 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2236 2195 10 %RANDOM
Rwork0.2192 ---
obs0.2196 19705 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 170.44 Å2 / Biso mean: 64.349 Å2 / Biso min: 32.88 Å2
Baniso -1Baniso -2Baniso -3
1--3.53 Å20 Å20 Å2
2--10.18 Å2-0 Å2
3----6.65 Å2
Refinement stepCycle: final / Resolution: 2.8→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3799 0 3 7 3809
Biso mean--64.52 46.84 -
Num. residues----520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123850
X-RAY DIFFRACTIONr_angle_refined_deg1.521.6195235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4065517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.46221.34194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.33915590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2921533
X-RAY DIFFRACTIONr_chiral_restr0.1110.2544
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022949
LS refinement shellResolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 177 -
Rwork0.397 1427 -
all-1604 -
obs--100 %

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