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- PDB-9wbp: Crystal Structure of Pseudomonas aeruginosa SuhB in complex with ... -

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Basic information

Entry
Database: PDB / ID: 9wbp
TitleCrystal Structure of Pseudomonas aeruginosa SuhB in complex with Adenosine 2'-monophosphate
ComponentsNus factor SuhB
KeywordsHYDROLASE / Pseudomonas aeruginosa SuhB / Inositol monophosphatase
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 / DNA-templated transcription / metal ion binding / RNA 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
ADENOSINE-2'-MONOPHOSPHATE / Nus factor SuhB
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYadav, V.K. / 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 in complex with Adenosine 2'-monophosphate
Authors: Yadav, V.K. / Bhattacharyya, S.
History
DepositionAug 14, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2026Provider: 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)60,2849
Polymers59,3372
Non-polymers9477
Water10,809600
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-59 kcal/mol
Surface area21560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.696, 90.051, 113.377
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 0 through 21 or resid 23 through 187 or resid 189 through 270))
d_2ens_1(chain "B" and (resid 0 through 21 or resid 23...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERARGARGAA0 - 212 - 23
d_12ILEILEARGARGAA23 - 18725 - 189
d_13ALAALALYSLYSAA189 - 270191 - 272
d_21SERSERARGARGBB0 - 212 - 23
d_22ILEILEPHEPHEBB23 - 16125 - 163
d_23ILEILEARGARGBB166 - 187168 - 189
d_24ALAALALYSLYSBB189 - 270191 - 272

NCS oper: (Code: givenMatrix: (-0.528966688236, 0.00719702789134, -0.848612070104), (0.000414317324299, -0.999961729494, -0.00873887230881), (-0.848642487198, -0.00497416702636, 0.52894346256)Vector: ...NCS oper: (Code: given
Matrix: (-0.528966688236, 0.00719702789134, -0.848612070104), (0.000414317324299, -0.999961729494, -0.00873887230881), (-0.848642487198, -0.00497416702636, 0.52894346256)
Vector: 24.1467669911, -0.105785084913, 13.4395204538)

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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.: 2 / Mutation: F71L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Gene: suhB, PA3818 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HXI4, inositol-phosphate phosphatase
#2: Chemical ChemComp-2AM / ADENOSINE-2'-MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 600 / 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: 2.79 Å3/Da / Density % sol: 56.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: Sodium acetate trihydrate and PEG3350 / PH range: 4.5-5.0 / Temp details: Room temperature

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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: May 27, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 2→48.07 Å / Num. obs: 45736 / % possible obs: 98.9 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.028 / Rrim(I) all: 0.074 / Net I/σ(I): 14.6
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.402 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 6170 / CC1/2: 0.912 / Rpim(I) all: 0.241 / Rrim(I) all: 0.473 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SCALAdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.07 Å / SU ML: 0.2683 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.4219
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2544 2248 5.03 %
Rwork0.2032 42414 -
obs0.2058 44662 96.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.41 Å2
Refinement stepCycle: LAST / Resolution: 2→48.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4121 0 56 600 4777
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00744283
X-RAY DIFFRACTIONf_angle_d1.23855799
X-RAY DIFFRACTIONf_chiral_restr0.0539638
X-RAY DIFFRACTIONf_plane_restr0.0077754
X-RAY DIFFRACTIONf_dihedral_angle_d15.0876620
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.815756257267 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.040.39421310.32372408X-RAY DIFFRACTION89.4
2.04-2.090.32161480.26752535X-RAY DIFFRACTION94.51
2.09-2.140.31131380.24952677X-RAY DIFFRACTION98.98
2.14-2.20.29941240.31212643X-RAY DIFFRACTION97.46
2.2-2.270.59211400.50272317X-RAY DIFFRACTION85.82
2.27-2.340.47141210.38412238X-RAY DIFFRACTION82.42
2.34-2.420.2451410.23172701X-RAY DIFFRACTION99.79
2.42-2.520.25991570.21222711X-RAY DIFFRACTION100
2.52-2.630.26431530.21382711X-RAY DIFFRACTION99.9
2.63-2.770.2661320.19922714X-RAY DIFFRACTION99.96
2.77-2.950.22841550.19362736X-RAY DIFFRACTION99.93
2.95-3.170.23921550.19462721X-RAY DIFFRACTION99.97
3.17-3.490.2541310.18222781X-RAY DIFFRACTION100
3.49-40.23631450.16672760X-RAY DIFFRACTION99.69
4-5.040.15511390.13922818X-RAY DIFFRACTION99.76
5.04-48.070.20631380.1672943X-RAY DIFFRACTION99.84
Refinement TLS params.Method: refined / Origin x: 5.09544107383 Å / Origin y: 0.0410074699983 Å / Origin z: 18.9496965874 Å
111213212223313233
T0.192572599519 Å20.0410073821928 Å20.0395638881885 Å2-0.180673811819 Å20.0192286089076 Å2--0.18550813844 Å2
L1.49480218939 °20.118339396327 °20.634701101646 °2-0.691626212806 °20.0345507731962 °2--0.891290848941 °2
S0.00282018268843 Å °0.0537975084239 Å °-0.067212367485 Å °-0.0641964253704 Å °-0.00224863572202 Å °-0.0463926312711 Å °-0.00557053265449 Å °0.0332993813233 Å °0.0023295543781 Å °
Refinement TLS groupSelection details: all

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