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- PDB-4g61: Crystal structure of IMPase/NADP phosphatase complexed with Mg2+ ... -

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Basic information

Entry
Database: PDB / ID: 4g61
TitleCrystal structure of IMPase/NADP phosphatase complexed with Mg2+ and phosphate
ComponentsInositol monophosphatase family protein
KeywordsHYDROLASE / IMPase / NADP phosphatase / FIG superfamily
Function / homology
Function and homology information


D-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
Similarity search - Domain/homology
1-HYDROXYSULFANYL-4-MERCAPTO-BUTANE-2,3-DIOL / PHOSPHATE ION / :
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsBhattacharyya, S. / Dutta, D. / Ghosh, A.K. / 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
DepositionJul 18, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _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 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)63,89819
Polymers62,4322
Non-polymers1,46617
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint0 kcal/mol
Surface area21760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.709, 63.054, 141.617
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 / IMPase / NADP phosphatase


Mass: 31215.881 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MSSA476 / Gene: 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 , 8 types, 268 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / 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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-DTO / 1-HYDROXYSULFANYL-4-MERCAPTO-BUTANE-2,3-DIOL


Mass: 170.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3S2
#7: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.17 Å3/Da / Density % sol: 43.34 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M MgCl2 6H2O, 0.1M HEPES pH 8.0, 18% (w/v) PEG 3350, 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: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 25, 2012
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→70.809 Å / Num. all: 24511 / Num. obs: 24511 / % possible obs: 98.3 % / Redundancy: 7.1 % / Rsym value: 0.093 / Net I/σ(I): 20.9
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
2.3-2.427.10.440.4081.92548935890.1640.440.4085.4100
2.42-2.577.10.3030.2812.72406733770.1130.3030.2817.6100
2.57-2.757.20.2290.2123.62292832030.0850.2290.2129.8100
2.75-2.977.20.170.1574.82125229590.0630.170.15713100
2.97-3.257.20.1190.116.91987427630.0440.1190.1118.2100
3.25-3.647.10.0770.07210.61744124560.0290.0770.07227.498.1
3.64-4.27.10.0550.05114.71353819020.0210.0550.05137.185.1
4.2-5.147.10.0370.03421.41355419080.0140.0370.03449.7100
5.14-7.2770.0460.04317.51054515090.0170.0460.04340.1100
7.27-19.6756.50.0230.02129.754548450.0090.0230.0216495.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.4 Å19.67 Å
Translation2.4 Å19.67 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→19.67 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.2157 / WRfactor Rwork: 0.1513 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8377 / SU B: 14.752 / SU ML: 0.169 / SU R Cruickshank DPI: 0.3952 / SU Rfree: 0.2661 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.395 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2553 1235 5 %RANDOM
Rwork0.176 ---
obs0.18 24474 98.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 78.51 Å2 / Biso mean: 21.499 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å20 Å2
2---0.07 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4184 0 85 251 4520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0224373
X-RAY DIFFRACTIONr_angle_refined_deg1.8331.9675896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4815528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.64625.545202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.87815769
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.1011511
X-RAY DIFFRACTIONr_chiral_restr0.120.2649
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213228
X-RAY DIFFRACTIONr_mcbond_it0.8251.52627
X-RAY DIFFRACTIONr_mcangle_it1.47324239
X-RAY DIFFRACTIONr_scbond_it2.68631746
X-RAY DIFFRACTIONr_scangle_it4.1624.51655
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 94 -
Rwork0.196 1714 -
all-1808 -
obs--100 %
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)
11.1968-0.0876-0.12560.4394-0.00811.17470.00110.00750.08490.0450.0119-0.021-0.2126-0.1726-0.01290.06820.040.01060.02820.00330.01516.151928.09618.0517
21.46710.4775-0.08450.9528-0.46131.31970.0655-0.0168-0.22050.0979-0.0923-0.16410.09610.04430.02680.05660.0049-0.03960.02-0.00570.088721.73821.305218.6023
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 265
2X-RAY DIFFRACTION2B4 - 265

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