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- PDB-4ptk: Crystal structure of Staphylococcal IMPase-I complex with 3Mg2+ a... -

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Basic information

Entry
Database: PDB / ID: 4ptk
TitleCrystal structure of Staphylococcal IMPase-I complex with 3Mg2+ and Phosphate
ComponentsInositol monophosphatase family protein
KeywordsHYDROLASE / IMPase product complex
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 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.503 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
DepositionMar 11, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 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 1.2Nov 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)62,95212
Polymers62,4322
Non-polymers52010
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-76 kcal/mol
Surface area21690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.428, 62.455, 140.497
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#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 (bacteria) / Strain: MSSA476 / Gene: SAS2203 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q6G709
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


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.: 6 / Source method: obtained synthetically / Formula: Mg
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.12 Å3/Da / Density % sol: 42.07 % / Mosaicity: 0 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M MgCl2, 0.1M HEPES pH8,18% (W/V) PEG 3350, Soaked with 0.1M HEPES pH8, 18% (W/V) PEG 3350, 10% Glycerol for 24 hours, 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 / Details: mirror
RadiationMonochromator: varimax (osmic mirror) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.503→140.497 Å / Num. all: 18411 / Num. obs: 18411 / % possible obs: 97.3 % / Redundancy: 7.6 % / Rsym value: 0.149 / Net I/σ(I): 14.3
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.503-2.647.70.6951.11986425880.2660.6953.395.7
2.64-2.87.70.4921.61898424530.1880.4924.596
2.8-2.997.70.3772.11805823480.1450.3775.896.6
2.99-3.237.70.2622.91677421880.1010.2628.497.3
3.23-3.547.60.1475.21554620390.0570.1471497.8
3.54-3.967.60.1017.71424118780.0390.10119.898
3.96-4.577.50.06611.61248416610.0260.06627.698.5
4.57-5.67.40.06312.31061114310.0250.06328.499
5.6-7.917.20.07810831211490.0310.07823.399.4
7.91-46.6766.50.03122.144226760.0130.0314798.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
MOLREPphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QMF

3qmf


Resolution: 2.503→46.72 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.894 / WRfactor Rfree: 0.2043 / WRfactor Rwork: 0.1465 / FOM work R set: 0.858 / SU B: 9.013 / SU ML: 0.2 / SU R Cruickshank DPI: 1.8181 / SU Rfree: 0.3283 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.818 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2569 953 5.2 %RANDOM
Rwork0.1771 ---
obs0.181 18387 96.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.39 Å2 / Biso mean: 27.592 Å2 / Biso min: 9.78 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å2-0 Å2
2--0.89 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 2.503→46.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4191 0 28 72 4291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194301
X-RAY DIFFRACTIONr_bond_other_d0.0010.024134
X-RAY DIFFRACTIONr_angle_refined_deg1.8071.9595814
X-RAY DIFFRACTIONr_angle_other_deg0.86939528
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7355521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.30925.821201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.58115778
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.816158
X-RAY DIFFRACTIONr_chiral_restr0.0960.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024841
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02975
LS refinement shellResolution: 2.503→2.568 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 62 -
Rwork0.204 1220 -
all-1282 -
obs--94.61 %

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