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- PDB-8cib: Structural and functional analysis of the Pseudomonas aeruginosa ... -

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Basic information

Entry
Database: PDB / ID: 8cib
TitleStructural and functional analysis of the Pseudomonas aeruginosa PA1677 protein
ComponentsCysteine hydrolase
KeywordsUNKNOWN FUNCTION / Pseudomonas aeruginosa / carbon catabolite repression / Crc antagonist
Function / homologystreptothricin hydrolase / : / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase domain / hydrolase activity / ACETATE ION / LYSINE / Cysteine hydrolase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsSonnleitner, E. / Brear, P. / Luisi, B.F. / Blasi, U.
Funding support United Kingdom, Austria, 2items
OrganizationGrant numberCountry
Wellcome Trust200873/Z/16/Z United Kingdom
Austrian Science FundP28711-B22 Austria
CitationJournal: Front Microbiol / Year: 2023
Title: Catabolite repression control protein antagonist, a novel player in Pseudomonas aeruginosa carbon catabolite repression control.
Authors: Sonnleitner, E. / Bassani, F. / Cianciulli Sesso, A. / Brear, P. / Lilic, B. / Davidovski, L. / Resch, A. / Luisi, B.F. / Moll, I. / Blasi, U.
History
DepositionFeb 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine hydrolase
B: Cysteine hydrolase
C: Cysteine hydrolase
D: Cysteine hydrolase
E: Cysteine hydrolase
F: Cysteine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,24614
Polymers134,3316
Non-polymers9158
Water17,060947
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15210 Å2
ΔGint-145 kcal/mol
Surface area44260 Å2
Unit cell
Length a, b, c (Å)85.284, 245.260, 126.262
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

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Components

#1: Protein
Cysteine hydrolase


Mass: 22388.492 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: yddQ1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A072ZIR4
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 947 / 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: 2.46 Å3/Da / Density % sol: 49.95 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Sodium HEPES; MOPS (acid) 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350 0.2M DL-Glutamic acid monohydrate; 0.2M DL Alanine; 0.2M Glycine; 0.2M DL-Lysine monohydrochloride; 0.2M DL-Serine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.78→122.63 Å / Num. obs: 120918 / % possible obs: 96.2 % / Redundancy: 7 % / CC1/2: 0.989 / Rmerge(I) obs: 0.263 / Rpim(I) all: 0.107 / Rrim(I) all: 0.285 / Χ2: 0.97 / Net I/σ(I): 6.7 / Num. measured all: 845570
Reflection shellResolution: 1.78→1.88 Å / % possible obs: 73.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 1.302 / Num. measured all: 58756 / Num. unique obs: 13457 / CC1/2: 0.416 / Rpim(I) all: 0.643 / Rrim(I) all: 1.462 / Χ2: 0.93 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC8.0.005refinement
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→122.63 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.277 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20836 6093 5.1 %RANDOM
Rwork0.17416 ---
obs0.1759 114353 95.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.632 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å20 Å2
2---0.62 Å20 Å2
3----0.13 Å2
Refinement stepCycle: 1 / Resolution: 1.78→122.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8804 0 62 947 9813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0139106
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158883
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.64612387
X-RAY DIFFRACTIONr_angle_other_deg1.5641.57420365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.16751184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92920.909473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.581151443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3181585
X-RAY DIFFRACTIONr_chiral_restr0.0730.21201
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210521
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022037
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8592.124749
X-RAY DIFFRACTIONr_mcbond_other1.8582.124748
X-RAY DIFFRACTIONr_mcangle_it2.8813.1695928
X-RAY DIFFRACTIONr_mcangle_other2.8813.175929
X-RAY DIFFRACTIONr_scbond_it2.8882.5254356
X-RAY DIFFRACTIONr_scbond_other2.8882.5254357
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6313.6466460
X-RAY DIFFRACTIONr_long_range_B_refined6.68327.3349962
X-RAY DIFFRACTIONr_long_range_B_other6.37826.3959615
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.784→1.83 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 322 -
Rwork0.313 6082 -
obs--69.38 %

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