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- PDB-8wip: Crystal Structure of Pseudomonas aeruginosa SuhB in its apo form. -

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Basic information

Entry
Database: PDB / ID: 8wip
TitleCrystal Structure of Pseudomonas aeruginosa SuhB in its apo form.
ComponentsNus factor SuhB
KeywordsHYDROLASE / Inositol monophosphatase / Extragenic Suppressor.
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 / IMIDAZOLE / Nus factor SuhB
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 its apo form.
Authors: Yadav, V.K. / Maji, S. / Shukla, M. / Bhattacharyya, S.
History
DepositionSep 25, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2024Provider: 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
B: Nus factor SuhB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5245
Polymers59,3372
Non-polymers1873
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-8 kcal/mol
Surface area20960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.784, 89.358, 98.985
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid -1 through 270)
d_2ens_1chain "B"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: -1 - 270 / Label seq-ID: 1 - 272

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (0.0545148034578, -0.0318432965113, -0.998005080484), (-0.0183992572918, -0.999353697779, 0.0308812899109), (-0.998343429655, 0.0166790648043, -0.0550654634248)Vector: - ...NCS oper: (Code: given
Matrix: (0.0545148034578, -0.0318432965113, -0.998005080484), (-0.0183992572918, -0.999353697779, 0.0308812899109), (-0.998343429655, 0.0166790648043, -0.0550654634248)
Vector: -55.5575312642, 23.2664239983, -59.287097318)

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Components

#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) / Gene: suhB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HXI4
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.42 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: Sodium acetate trihydrate, PEG 3350, pH 5.0 / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: Liquid Nitrogen Flow / 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 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.6→46.71 Å / Num. obs: 18511 / % possible obs: 99.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 37.54 Å2 / CC1/2: 0.997 / Net I/σ(I): 15.1
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 4.2 % / Num. unique obs: 2666 / CC1/2: 0.905 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→44.68 Å / SU ML: 0.2446 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.0663
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2468 853 4.62 %
Rwork0.2074 17611 -
obs0.2092 18464 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.31 Å2
Refinement stepCycle: LAST / Resolution: 2.6→44.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4154 0 13 139 4306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01124245
X-RAY DIFFRACTIONf_angle_d1.5115735
X-RAY DIFFRACTIONf_chiral_restr0.0856630
X-RAY DIFFRACTIONf_plane_restr0.0256757
X-RAY DIFFRACTIONf_dihedral_angle_d7.55594
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.911201705806 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.760.28071350.24172906X-RAY DIFFRACTION99.93
2.76-2.980.32881250.24832912X-RAY DIFFRACTION99.97
2.98-3.280.31851510.24922879X-RAY DIFFRACTION99.87
3.28-3.750.25221630.21512903X-RAY DIFFRACTION99.77
3.75-4.720.19671300.17712953X-RAY DIFFRACTION99.04
4.72-44.680.21131490.18633058X-RAY DIFFRACTION98.89
Refinement TLS params.Method: refined / Origin x: 25.2254219216 Å / Origin y: 11.8841091544 Å / Origin z: -17.6188862428 Å
111213212223313233
T0.206608556802 Å2-0.0344711864675 Å2-0.00207643083524 Å2-0.219922181506 Å2-0.0124791010644 Å2--0.205090436864 Å2
L1.28872885744 °2-0.418581011211 °20.778153815322 °2-1.45457112604 °2-0.220098534867 °2--1.39969789068 °2
S-0.0305811668126 Å °-0.115504241171 Å °-0.0304261568821 Å °0.0204100788637 Å °0.0619464700857 Å °0.146787446829 Å °0.0318261180771 Å °-0.114799866132 Å °-0.0290730208043 Å °
Refinement TLS groupSelection details: all

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