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- PDB-4i3y: Crystal structure of Staphylococcal inositol monophosphatase-1: 1... -

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Basic information

Entry
Database: PDB / ID: 4i3y
TitleCrystal structure of Staphylococcal inositol monophosphatase-1: 100 mM LiCl soaked inhibitory complex
ComponentsInositol monophosphatase family protein
KeywordsHYDROLASE / Inositol monophosphatase / penta layer repeat of alpha/beta stretches / Magnesium binding / Cytoplasmic
Function / homologyD-Maltodextrin-Binding Protein; domain 2 - #80 / Fructose-1,6-Bisphosphatase, subunit A, domain 1 / Fructose-1,6-Bisphosphatase; Chain A, domain 1 / D-Maltodextrin-Binding Protein; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta / PHOSPHATE ION / :
Function and homology information
Biological speciesStaphylococcus aureus subsp. aureus MSSA476 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.04 Å
AuthorsDutta, A. / Bhattacharyya, S. / Dutta, D. / Das, A.K.
CitationJournal: Febs J. / Year: 2014
Title: Structural elucidation of the binding site and mode of inhibition of Li(+) and Mg(2+) in inositol monophosphatase.
Authors: Dutta, A. / Bhattacharyya, S. / Dutta, D. / Das, A.K.
History
DepositionNov 26, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inositol monophosphatase family protein
B: Inositol monophosphatase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,76216
Polymers62,4322
Non-polymers1,33014
Water3,927218
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Inositol monophosphatase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1269
Polymers31,2161
Non-polymers9108
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Inositol monophosphatase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6367
Polymers31,2161
Non-polymers4206
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.136, 62.819, 141.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Inositol monophosphatase family protein


Mass: 31215.881 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus MSSA476 (bacteria)
Strain: MSSA476 / Gene: Inositol monophosphatase (SAS2203), SAS2203 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q6G709, inositol-phosphate phosphatase

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Non-polymers , 5 types, 232 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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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: 42.57 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M MgCl2, 0.1M HEPES, 20%(w/v) PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 26, 2012 / Details: VariMax
RadiationMonochromator: VariMax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.04→70.79 Å / Num. all: 34974 / Num. obs: 34974 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rsym value: 0.109 / Net I/σ(I): 17.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.04-2.1570.630.5831.43540250370.2350.630.5833.599.9
2.15-2.287.10.430.39823367847520.160.430.3985.2100
2.28-2.447.10.3310.3072.63206944930.1230.3310.3076.7100
2.44-2.637.20.2430.2263.53003041990.090.2430.2269100
2.63-2.887.20.1670.1555.12784638670.0620.1670.15512.8100
2.88-3.237.20.1140.1067.42537535160.0420.1140.10618.3100
3.23-3.727.20.0630.05913.12257931300.0230.0630.05932100
3.72-4.567.10.0410.03820.11912726760.0150.0410.03845.2100
4.56-6.457.10.0380.03621.21490921090.0140.0380.03645.7100
6.45-19.5866.60.0260.02427.4794011950.010.0260.02458.796.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.25 Å19.59 Å
Translation2.25 Å19.59 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QMF

3qmf


Resolution: 2.04→19.59 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.912 / WRfactor Rfree: 0.2024 / WRfactor Rwork: 0.1506 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8368 / SU B: 4.852 / SU ML: 0.132 / SU R Cruickshank DPI: 0.2092 / SU Rfree: 0.1904 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.209 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2484 1753 5 %RANDOM
Rwork0.1841 ---
obs0.1873 34929 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.89 Å2 / Biso mean: 22.116 Å2 / Biso min: 8.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å2-0 Å2-0 Å2
2---0.36 Å2-0 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 2.04→19.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4215 0 65 218 4498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194386
X-RAY DIFFRACTIONr_angle_refined_deg2.1511.9655915
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1695530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.45525.588204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.19115790
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1391511
X-RAY DIFFRACTIONr_chiral_restr0.1410.2653
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213249
LS refinement shellResolution: 2.04→2.093 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 125 -
Rwork0.222 2425 -
all-2550 -
obs--99.73 %

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