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- PDB-4i40: crystal structure of Staphylococcal inositol monophosphatase-1: 5... -

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Basic information

Entry
Database: PDB / ID: 4i40
Titlecrystal structure of Staphylococcal inositol monophosphatase-1: 50mM LiCl inhibited complex
ComponentsInositol monophosphatase family protein
KeywordsHYDROLASE / Inositol monophosphatase-1 / Li inhibition / 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 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 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 27, 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)63,31613
Polymers62,4322
Non-polymers88411
Water2,360131
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)31,6707
Polymers31,2161
Non-polymers4546
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Inositol monophosphatase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6466
Polymers31,2161
Non-polymers4305
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.977, 62.397, 140.638
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 (bacteria)
Strain: MSSA476 / Gene: Inositol monophosphatase / 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, 142 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.11 Å3/Da / Density % sol: 41.64 % / Mosaicity: 0.13 °
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

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 19, 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: 2.5→70.319 Å / Num. all: 18941 / Num. obs: 18941 / % possible obs: 99.7 % / Redundancy: 6.6 % / Rsym value: 0.16 / Net I/σ(I): 11.9
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
2.5-2.636.60.6320.5821.31764226840.2430.6320.5823.599.3
2.63-2.796.70.4740.4371.81733225790.1810.4740.4374.7100
2.79-2.986.70.3780.3492.21642424480.1450.3780.3495.9100
2.98-3.226.70.270.2493.11518322510.1030.270.2498.1100
3.22-3.536.70.1680.15551416421120.0640.1680.15512.6100
3.53-3.956.70.1160.1077.11278819160.0440.1160.10717.1100
3.95-4.566.70.0840.0779.61128416920.0320.0840.07722100
4.56-5.586.60.0810.0749.9956414590.0310.0810.07422.2100
5.58-7.96.40.1060.0977.9747611640.0410.1060.09717.6100
7.9-19.72860.0430.03916.537966360.0180.0430.03933.893.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QMF

3qmf


Resolution: 2.5→19.74 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.891 / WRfactor Rfree: 0.2175 / WRfactor Rwork: 0.1478 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8466 / SU B: 9.32 / SU ML: 0.21 / SU R Cruickshank DPI: 1.2968 / SU Rfree: 0.3227 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.297 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2573 975 5.2 %RANDOM
Rwork0.1754 ---
obs0.1794 18907 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.39 Å2 / Biso mean: 22.6497 Å2 / Biso min: 3.23 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å2-0 Å2-0 Å2
2---0.48 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4172 0 51 131 4354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194303
X-RAY DIFFRACTIONr_bond_other_d0.0010.024122
X-RAY DIFFRACTIONr_angle_refined_deg1.7241.9625809
X-RAY DIFFRACTIONr_angle_other_deg0.89539499
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8125522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.17825.758198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.68315763
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.348158
X-RAY DIFFRACTIONr_chiral_restr0.0970.2641
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024832
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02972
LS refinement shellResolution: 2.5→2.562 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 80 -
Rwork0.208 1245 -
all-1325 -
obs--98.37 %

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