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- PDB-9j90: Crystal structure of Pseudomonas aeruginosa SuhB complexed with G... -

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Basic information

Entry
Database: PDB / ID: 9j90
TitleCrystal structure of Pseudomonas aeruginosa SuhB complexed with Gallic acid in orthorhombic space group
ComponentsNus factor SuhB
KeywordsHYDROLASE / SuhB / Inositol monophosphatase / Gallic acid / Phytochemical
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
(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / 3,4,5-trihydroxybenzoic acid / Nus factor SuhB
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsYadav, V.K. / Shukla, M. / Maji, S. / Bhattacharyya, S.
Funding support India, 1items
OrganizationGrant numberCountry
Other governmentS-12011/12/2021-SCHEME India
CitationJournal: To Be Published
Title: Crystal structure of Pseudomonas aeruginosa SuhB complexed with Gallic acid in orthorhombic space group
Authors: Yadav, V.K. / Shukla, M. / Maji, S. / Bhattacharyya, S.
History
DepositionAug 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,3734
Polymers59,0492
Non-polymers3242
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-8 kcal/mol
Surface area20500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.681, 90.108, 90.453
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nus factor SuhB / Inositol-1-monophosphatase / I-1-Pase / IMPase / Inositol-1-phosphatase


Mass: 29524.529 Da / Num. of mol.: 2 / Mutation: F71L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: suhB / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HXI4, inositol-phosphate phosphatase
#2: Chemical ChemComp-DTV / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#3: Chemical ChemComp-GDE / 3,4,5-trihydroxybenzoic acid / Gallate


Mass: 170.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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 % sol: 35.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: PEG 3350, Sodium acetate tri-hydrate

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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: 0.97893 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 24, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 2.8→47.42 Å / Num. obs: 11742 / % possible obs: 99.9 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.031 / Rrim(I) all: 0.083 / Net I/σ(I): 21.2 / Num. measured all: 83327
Reflection shellResolution: 2.8→2.95 Å / % possible obs: 100 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.433 / Num. measured all: 12381 / Num. unique obs: 1685 / CC1/2: 0.913 / Rpim(I) all: 0.171 / Rrim(I) all: 0.466 / Net I/σ(I) obs: 4.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SCALAdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→35.13 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.915 / SU B: 32.268 / SU ML: 0.297 / Cross valid method: THROUGHOUT / ESU R Free: 0.412 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23759 571 4.9 %RANDOM
Rwork0.17879 ---
obs0.1818 11128 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.006 Å2
Baniso -1Baniso -2Baniso -3
1-3.87 Å20 Å2-0 Å2
2---3.12 Å20 Å2
3----0.75 Å2
Refinement stepCycle: 1 / Resolution: 2.8→35.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4066 0 20 32 4118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134162
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173966
X-RAY DIFFRACTIONr_angle_refined_deg1.7111.6355623
X-RAY DIFFRACTIONr_angle_other_deg1.6061.589078
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3185527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.37620.87230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.80215678
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7691538
X-RAY DIFFRACTIONr_chiral_restr0.1080.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024780
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021004
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_it2.8274.562120
X-RAY DIFFRACTIONr_mcbond_other2.8264.5592119
X-RAY DIFFRACTIONr_mcangle_it4.5156.8242643
X-RAY DIFFRACTIONr_mcangle_other4.5156.8252644
X-RAY DIFFRACTIONr_scbond_it3.0565.1042042
X-RAY DIFFRACTIONr_scbond_other3.0425.1012040
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0517.52981
X-RAY DIFFRACTIONr_long_range_B_refined9.8188.10517687
X-RAY DIFFRACTIONr_long_range_B_other9.8188.10317684
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 7993 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 49 -
Rwork0.218 799 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.571-0.5467-0.14870.859-0.21950.7027-0.0012-0.040.03260.06840.1347-0.0281-0.028-0.1031-0.13350.0336-0.0081-0.02110.09040.03650.11231.1474-6.4011-5.7867
20.58230.3432-0.22520.61920.46241.1853-0.01890.0514-0.054-0.01150.0463-0.06050.00690.0743-0.02740.006-0.02150.00390.1003-0.00230.098515.5772-15.2639-28.7381
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B1 - 301
2X-RAY DIFFRACTION2A1 - 301

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