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- PDB-5i3s: Crystal structure of Staphylococcal IMPase-II -

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Basic information

Entry
Database: PDB / ID: 5i3s
TitleCrystal structure of Staphylococcal IMPase-II
ComponentsInositol monophosphatase family protein
KeywordsHYDROLASE / IMPase / FIG superfamily / sugar phosphatase fold / staphylococcus aureus
Function / homology
Function and homology information


Inositol monophosphatase, metal-binding site / Inositol monophosphatase family signature 1. / Inositol monophosphatase-like / Inositol monophosphatase family / 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
PHOSPHATE ION / : / Inositol monophosphatase family protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsDutta, A. / Bhattacharyya, S. / Dutta, D. / Das, A.K.
CitationJournal: To Be Published
Title: Crystal structure of Staphylococcal IMPase-II
Authors: Dutta, A. / Bhattacharyya, S. / Dutta, D. / Das, A.K.
History
DepositionFeb 11, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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
C: Inositol monophosphatase family protein
D: Inositol monophosphatase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,3298
Polymers121,9494
Non-polymers3804
Water7,278404
1
A: Inositol monophosphatase family protein
B: Inositol monophosphatase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1644
Polymers60,9742
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Inositol monophosphatase family protein
D: Inositol monophosphatase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1644
Polymers60,9742
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.004, 131.391, 80.901
Angle α, β, γ (deg.)90.000, 104.430, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Inositol monophosphatase family protein


Mass: 30487.246 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain MSSA476) (bacteria)
Strain: MSSA476 / Gene: SAS1042 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: A0A0J9WZD1, UniProt: A0A1I9GET0*PLUS
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.3M Ammonium dihydrogen phosphate, 0.1M Bis-Tris pH 6.0, 25% (w/v) PEG 3350

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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 13, 2013
RadiationMonochromator: varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.202→78.349 Å / Num. all: 56328 / Num. obs: 56328 / % possible obs: 98.4 % / Redundancy: 7.6 % / Rpim(I) all: 0.046 / Rrim(I) all: 0.127 / Rsym value: 0.118 / Net I/av σ(I): 6.298 / Net I/σ(I): 16.7 / Num. measured all: 426223
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.2-2.327.60.5581.46093680600.2160.5980.5583.496.5
2.32-2.467.60.4641.75871776910.1780.4970.4644.897.7
2.46-2.637.60.3022.65553372680.1160.3240.3027.198.3
2.63-2.847.60.2143.65184267860.0820.2290.2149.798.6
2.84-3.117.60.1445.44804563150.0560.1540.14414.198.9
3.11-3.487.60.0928.54346257250.0360.0980.09220.799.4
3.48-4.027.50.07110.63779950720.0280.0760.07127.999.7
4.02-4.927.50.03919.33215742850.0150.0420.03942.399.9
4.92-6.967.50.04217.12511233450.0170.0450.04238.7100
6.96-19.5877.10.02623.21262017810.0110.0280.02654.995.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation19.59 Å2.25 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
SCALA3.3.20data scaling
MOLREP11.0.05phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QFL

3qfl


Resolution: 2.2→78.35 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.863 / WRfactor Rfree: 0.2411 / WRfactor Rwork: 0.1929 / FOM work R set: 0.7645 / SU B: 7.586 / SU ML: 0.184 / SU R Cruickshank DPI: 0.3309 / SU Rfree: 0.2519 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.331 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2826 2812 5.1 %RANDOM
Rwork0.2286 ---
obs0.2313 52827 97.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.14 Å2 / Biso mean: 27.908 Å2 / Biso min: 7.72 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0.07 Å2
2--0.86 Å2-0 Å2
3----0.73 Å2
Refinement stepCycle: final / Resolution: 2.2→78.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7776 0 20 404 8200
Biso mean--18.77 32.49 -
Num. residues----1027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0197953
X-RAY DIFFRACTIONr_bond_other_d0.0020.027399
X-RAY DIFFRACTIONr_angle_refined_deg1.7871.95510844
X-RAY DIFFRACTIONr_angle_other_deg1.124316929
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.04851016
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67725.331362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.933151203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8081527
X-RAY DIFFRACTIONr_chiral_restr0.1230.21232
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219241
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021808
X-RAY DIFFRACTIONr_mcbond_it2.0912.7074097
X-RAY DIFFRACTIONr_mcbond_other2.0812.7064096
X-RAY DIFFRACTIONr_mcangle_it3.2394.045102
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.698 203 -
Rwork0.673 3557 -
all-3760 -
obs--88.8 %

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