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- PDB-8wdq: Crystal Structure of Pseudomonas aeruginosa SuhB in complex with ... -

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Basic information

Entry
Database: PDB / ID: 8wdq
TitleCrystal Structure of Pseudomonas aeruginosa SuhB in complex with D-myo-inositol-1-phosphate
ComponentsNus factor SuhB
KeywordsHYDROLASE / Inositol monophosphatase / SuhB / Pseudomonas aeruginosa / D-myo-inositol-1-phosphate
Function / homology
Function and homology information


inositol-phosphate phosphatase / inositol monophosphate 1-phosphatase activity / inositol metabolic process / phosphatidylinositol phosphate biosynthetic process / transcription antitermination / ribosome biogenesis / signal transduction / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
Inositol monophosphatase SuhB-like / Inositol monophosphatase / Inositol monophosphatase, conserved site / Inositol monophosphatase family signature 2. / Inositol monophosphatase, metal-binding site / Inositol monophosphatase family signature 1. / Inositol monophosphatase-like / Inositol monophosphatase family
Similarity search - Domain/homology
ACETATE ION / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / D-MYO-INOSITOL-1-PHOSPHATE / HYDROGEN PEROXIDE / Nus factor SuhB
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYadav, V.K. / Maji, S. / Shukla, M. / Bhattacharyya, S.
Funding support India, 1items
OrganizationGrant numberCountry
Other governmentS-12011/12/2021 India
CitationJournal: To Be Published
Title: Crystal Structure of Pseudomonas aeruginosa SuhB in complex with D-myo-inositol-1-phosphate
Authors: Yadav, V.K. / Maji, S. / Shukla, M. / Bhattacharyya, S.
History
DepositionSep 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nus factor SuhB
B: Nus factor SuhB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,58217
Polymers59,3372
Non-polymers1,24515
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.620, 88.690, 97.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Nus factor SuhB


Mass: 29668.654 Da / Num. of mol.: 2 / Mutation: F71L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: suhB / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HXI4

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Non-polymers , 8 types, 312 molecules

#2: Chemical ChemComp-IPD / D-MYO-INOSITOL-1-PHOSPHATE


Mass: 258.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H11O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-DTU / (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: Ca
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.4 Å3/Da / Density % sol: 48.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Sodium acetate trihydrate/acetate buffer, PEG 3350, pH 4.5
Temp details: Room temeperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9789 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.2→54.48 Å / Num. obs: 29259 / % possible obs: 98.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 20.61 Å2 / CC1/2: 0.988 / Net I/σ(I): 7.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.9 % / Num. unique obs: 4112 / CC1/2: 0.866 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→52.75 Å / SU ML: 0.1708 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.7624
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2203 1436 4.91 %
Rwork0.1723 27786 -
obs0.1747 29222 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.64 Å2
Refinement stepCycle: LAST / Resolution: 2.2→52.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4176 0 67 297 4540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414329
X-RAY DIFFRACTIONf_angle_d0.76125852
X-RAY DIFFRACTIONf_chiral_restr0.0585648
X-RAY DIFFRACTIONf_plane_restr0.0062766
X-RAY DIFFRACTIONf_dihedral_angle_d7.0012611
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.280.26151290.19612683X-RAY DIFFRACTION96.63
2.28-2.370.2471420.18832686X-RAY DIFFRACTION97.18
2.37-2.480.22411350.17922698X-RAY DIFFRACTION97.39
2.48-2.610.22471440.18062731X-RAY DIFFRACTION98.22
2.61-2.770.22191610.18622760X-RAY DIFFRACTION98.98
2.77-2.990.23421450.17322778X-RAY DIFFRACTION99.49
2.99-3.290.23181420.17932796X-RAY DIFFRACTION99.56
3.29-3.760.23011380.16752825X-RAY DIFFRACTION99.76
3.76-4.740.18691440.14532856X-RAY DIFFRACTION99.67
4.74-52.750.2071560.17492973X-RAY DIFFRACTION99.46
Refinement TLS params.Method: refined / Origin x: -25.1634084871 Å / Origin y: 11.8341978028 Å / Origin z: -31.4932678439 Å
111213212223313233
T0.107277839356 Å20.0215821061258 Å20.0051716884282 Å2-0.111051024162 Å20.0165412409401 Å2--0.105182982325 Å2
L0.796796123191 °20.152276158849 °20.525609371309 °2-0.822936304024 °20.0050244333596 °2--0.866474151446 °2
S-0.0197104418174 Å °0.0184296243316 Å °0.00803169435169 Å °0.0188764264038 Å °0.0317750510206 Å °-0.0417013347212 Å °0.0537590912183 Å °0.0523482600853 Å °-0.00818810004373 Å °
Refinement TLS groupSelection details: all

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