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- PDB-3qmf: Crystal strucuture of an inositol monophosphatase family protein ... -

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Basic information

Entry
Database: PDB / ID: 3qmf
TitleCrystal strucuture of an inositol monophosphatase family protein (SAS2203) from Staphylococcus aureus MSSA476
ComponentsInositol monophosphatase family protein
KeywordsHYDROLASE / FIG superfamily / IMPase fold
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 / :
Function and homology information
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBhattacharyya, S. / Dutta, D. / Ghosh, A.K. / Das, A.K.
CitationJournal: Biochimie / Year: 2012
Title: Crystal structure of Staphylococcal dual specific inositol monophosphatase/NADP(H) phosphatase (SAS2203) delineates the molecular basis of substrate specificity
Authors: Bhattacharyya, S. / Dutta, D. / Saha, B. / Ghosh, A.K. / Das, A.K.
History
DepositionFeb 4, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Nov 1, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)63,2045
Polymers62,9162
Non-polymers2883
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.983, 68.350, 143.787
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Inositol monophosphatase family protein


Mass: 31458.146 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) / References: UniProt: Q6G709, inositol-phosphate phosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 1.95 Å3/Da / Density % sol: 36.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M Lithium sulphate, 0.1M HEPES pH 7.0, 20%(w/v) PEG 3350, VAPOR DIFFUSION, SITTING 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: Nov 14, 2010 / Details: mirrors
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.597→71.894 Å / Num. all: 15862 / Num. obs: 15691 / Observed criterion σ(F): 3 / Observed criterion σ(I): 3

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0095refinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
XDSdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2P3N

2p3n


Resolution: 2.6→19.67 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.87 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 27.287 / SU ML: 0.27 / Cross valid method: THROUGHOUT / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.269 785 5 %RANDOM
Rwork0.1947 ---
obs0.1984 15690 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 88.08 Å2 / Biso mean: 36.195 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å20 Å20 Å2
2---2.32 Å20 Å2
3---0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3992 0 15 79 4086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224095
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.9615543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.525498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.63225.789190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.39515721
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.895157
X-RAY DIFFRACTIONr_chiral_restr0.1090.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213060
X-RAY DIFFRACTIONr_mcbond_it0.571.52501
X-RAY DIFFRACTIONr_mcangle_it1.08324020
X-RAY DIFFRACTIONr_scbond_it1.6731594
X-RAY DIFFRACTIONr_scangle_it2.6634.51522
LS refinement shellResolution: 2.597→2.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 56 -
Rwork0.227 1046 -
all-1102 -
obs--95.16 %
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)
11.39370.4163-0.55542.0385-0.24792.30150.0762-0.02020.05530.1779-0.0107-0.1405-0.05060.1095-0.06550.02180.0038-0.01950.0136-0.01290.04138.087311.127635.8497
22.34430.4159-0.07143.51991.05942.1107-0.04820.1608-0.3927-0.60160.028-0.2730.09830.04490.02020.1975-0.00290.05650.1379-0.01610.08144.03243.17316.4806
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 265
2X-RAY DIFFRACTION2B2 - 265

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