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

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Basic information

Entry
Database: PDB / ID: 9jfc
TitleCrystal structure of Pseudomonas aeruginosa SuhB complexed with Gallic acid in monoclinic space group
ComponentsNus factor SuhB
KeywordsHYDROLASE / 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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / 3,4,5-trihydroxybenzoic acid / Nus factor SuhB
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 monoclinic space group
Authors: Yadav, V.K. / Shukla, M. / Maji, S. / Bhattacharyya, S.
History
DepositionSep 4, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 10, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nus factor SuhB
E: Nus factor SuhB
I: Nus factor SuhB
M: Nus factor SuhB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,12415
Polymers118,6754
Non-polymers1,44911
Water5,999333
1
A: Nus factor SuhB
E: Nus factor SuhB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1088
Polymers59,3372
Non-polymers7716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-9 kcal/mol
Surface area21140 Å2
MethodPISA
2
I: Nus factor SuhB
M: Nus factor SuhB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0167
Polymers59,3372
Non-polymers6795
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-5 kcal/mol
Surface area21050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.173, 90.603, 89.953
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
/ NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 29668.654 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: The starting two amino acids are cloning artifacts (coming from the plasmid vector).
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: suhB, PA3818 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HXI4, inositol-phosphate phosphatase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-GDE / 3,4,5-trihydroxybenzoic acid / Gallate


Mass: 170.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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 Matthews: 2.14 Å3/Da / Density % sol: 42.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Sodium acetate trihydrate

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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: 2.2→45.3 Å / Num. obs: 50522 / % possible obs: 99.6 % / Redundancy: 3.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.054 / Rrim(I) all: 0.104 / Net I/σ(I): 10.5 / Num. measured all: 189644
Reflection shellResolution: 2.2→2.32 Å / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.282 / Num. measured all: 27802 / Num. unique obs: 7363 / CC1/2: 0.928 / Rpim(I) all: 0.168 / Rrim(I) all: 0.329 / Net I/σ(I) obs: 4.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PHENIX1.21.2-5419refinement
SCALAdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→44.98 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.908 / SU B: 8.198 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23359 2505 5 %RANDOM
Rwork0.18235 ---
obs0.18475 47996 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.758 Å2
Baniso -1Baniso -2Baniso -3
1-22.61 Å20 Å21.35 Å2
2---11.4 Å2-0 Å2
3----11.21 Å2
Refinement stepCycle: 1 / Resolution: 2.2→44.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8288 0 94 333 8715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0138535
X-RAY DIFFRACTIONr_bond_other_d0.0020.0178114
X-RAY DIFFRACTIONr_angle_refined_deg1.9091.63511531
X-RAY DIFFRACTIONr_angle_other_deg1.4471.57918586
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.61151080
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34620.948464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.91151386
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8171576
X-RAY DIFFRACTIONr_chiral_restr0.0910.21078
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.029792
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022040
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_it1.6632.0874332
X-RAY DIFFRACTIONr_mcbond_other1.6632.0864331
X-RAY DIFFRACTIONr_mcangle_it2.5833.1255408
X-RAY DIFFRACTIONr_mcangle_other2.5833.1265409
X-RAY DIFFRACTIONr_scbond_it1.7212.264203
X-RAY DIFFRACTIONr_scbond_other1.7212.2614204
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6393.3346124
X-RAY DIFFRACTIONr_long_range_B_refined5.87939.68536646
X-RAY DIFFRACTIONr_long_range_B_other5.83439.67936511
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A78740.15
12E78740.15
21A79760.15
22I79760.15
31A79020.15
32M79020.15
41E79540.15
42I79540.15
51E78770.15
52M78770.15
61I79950.16
62M79950.16
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 201 -
Rwork0.248 3493 -
obs--99.22 %
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)
10.29450.19930.02350.6246-0.23570.3766-0.06150.00350.0131-0.05820.01420.0115-0.0236-0.02750.04730.0173-0.0015-0.01230.0313-0.0050.039915.3341.43839.138
20.4941-0.27160.1380.37580.14860.28970.0052-0.0229-0.02790.05210.031-0.02610.0461-0.0082-0.03620.02380.0039-0.01360.0249-0.00050.03928.673-8.46761.975
30.5021-0.2752-0.00460.2936-0.14850.53280.0142-0.00580.03430.04530.01280.0105-0.041-0.0171-0.02710.0258-0.00590.01950.02280.00220.05072.217-21.50816.926
40.30740.4028-0.00370.62980.21330.6476-0.03190.0136-0.0539-0.0360.0394-0.0354-0.01380.0457-0.00750.0137-0.0140.01980.03530.0050.060515.84-31.279-6.067
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 270
2X-RAY DIFFRACTION1A301 - 303
3X-RAY DIFFRACTION1E301
4X-RAY DIFFRACTION2E1 - 270
5X-RAY DIFFRACTION2A304
6X-RAY DIFFRACTION2E302
7X-RAY DIFFRACTION3I-1 - 270
8X-RAY DIFFRACTION3I401 - 402
9X-RAY DIFFRACTION3M301
10X-RAY DIFFRACTION4M-1 - 270
11X-RAY DIFFRACTION4I403
12X-RAY DIFFRACTION4M302

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