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- PDB-2fvz: Human Inositol Monophosphosphatase 2 -

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Basic information

Entry
Database: PDB / ID: 2fvz
TitleHuman Inositol Monophosphosphatase 2
ComponentsInositol monophosphatase 2
KeywordsHYDROLASE / Inositol metabolism / Inositol monophosphatase / structural genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


Synthesis of IP2, IP, and Ins in the cytosol / inositol biosynthetic process / inositol-phosphate phosphatase / inositol monophosphate 3-phosphatase activity / inositol monophosphate 4-phosphatase activity / inositol monophosphate 1-phosphatase activity / inositol metabolic process / phosphate-containing compound metabolic process / response to lithium ion / phosphatidylinositol phosphate biosynthetic process ...Synthesis of IP2, IP, and Ins in the cytosol / inositol biosynthetic process / inositol-phosphate phosphatase / inositol monophosphate 3-phosphatase activity / inositol monophosphate 4-phosphatase activity / inositol monophosphate 1-phosphatase activity / inositol metabolic process / phosphate-containing compound metabolic process / response to lithium ion / phosphatidylinositol phosphate biosynthetic process / signal transduction / protein homodimerization activity / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Inositol monophosphatase, lithium-sensitive / Inositol monophosphatase / Inositol monophosphatase, conserved site / Inositol monophosphatase family signature 2. / 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 ...Inositol monophosphatase, lithium-sensitive / Inositol monophosphatase / Inositol monophosphatase, conserved site / Inositol monophosphatase family signature 2. / 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
Inositol monophosphatase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOgg, D. / Hallberg, B.M. / Arrowsmith, C. / Berglund, H. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Graslund, S. / Hammarstrom, M. ...Ogg, D. / Hallberg, B.M. / Arrowsmith, C. / Berglund, H. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Graslund, S. / Hammarstrom, M. / Hogbom, M. / Holmberg-Schiavone, L. / Kotenyova, T. / Kursula, P. / Nilsson-Ehle, P. / Nordlund, P. / Nyman, T. / Persson, C. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / Van Den Berg, S. / Weigelt, J. / Thorsell, A.G. / Structural Genomics Consortium (SGC)
CitationJournal: To be published
Title: Structure of Human Inositol Monophosphatase 2
Authors: Thorsell, A.G. / Ogg, D. / Berglund, H. / Collins, R. / Ehn, M. / Flodin, S. / Graslund, S. / Hammarstrom, M. / Hogbom, M. / Holmberg-Schiavone, L. / Kotenyova, T. / Kursula, P. / Nilsson- ...Authors: Thorsell, A.G. / Ogg, D. / Berglund, H. / Collins, R. / Ehn, M. / Flodin, S. / Graslund, S. / Hammarstrom, M. / Hogbom, M. / Holmberg-Schiavone, L. / Kotenyova, T. / Kursula, P. / Nilsson-Ehle, P. / Persson, C. / Nordlund, P. / Nyman, T. / Sagemark, J. / Stenmark, P. / Van Den Berg, S. / Weigelt, J. / Hallberg, B.M.
History
DepositionJan 31, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inositol monophosphatase 2
B: Inositol monophosphatase 2
C: Inositol monophosphatase 2
D: Inositol monophosphatase 2


Theoretical massNumber of molelcules
Total (without water)119,7414
Polymers119,7414
Non-polymers00
Water0
1
A: Inositol monophosphatase 2
D: Inositol monophosphatase 2


Theoretical massNumber of molelcules
Total (without water)59,8712
Polymers59,8712
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-20 kcal/mol
Surface area19530 Å2
MethodPISA
2
B: Inositol monophosphatase 2
C: Inositol monophosphatase 2


Theoretical massNumber of molelcules
Total (without water)59,8712
Polymers59,8712
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-20 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.030, 96.950, 106.970
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Inositol monophosphatase 2 / / IMPase 2 / IMP 2 / Inositol-1(or 4)-monophosphatase 2 / Myo-inositol monophosphatase A2


Mass: 29935.322 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IMPA2, IMP.18P / Plasmid: pNIC-Bsa4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: O14732, inositol-phosphate phosphatase

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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: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 20% PEG 6000, 0.1M Hepes pH 6.8, 0.2M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-5 / Wavelength: 0.9075 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 4, 2005 / Details: Monochromator
RadiationMonochromator: Si-911 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9075 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 55439 / Num. obs: 51914 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.054 / Net I/σ(I): 16.85
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.433 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
SHELXrefinement
PDB_EXTRACT1.701data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→10 Å / Num. parameters: 30068 / Num. restraintsaints: 31372 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: This is a twinned structure. The twinning operator is (h,k,l) -> (h,-k,-l) and the twinning fraction is 0.5.
RfactorNum. reflection% reflectionSelection details
Rfree0.2974 861 1.7 %THIN SHELLS
Rwork0.211 ---
obs0.2141 50340 98.2 %-
all-50340 --
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Displacement parametersBiso mean: 57.306 Å2
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7516 0 0 0 7516
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.021
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.033
X-RAY DIFFRACTIONs_zero_chiral_vol0.097
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.032
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.06
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.104
X-RAY DIFFRACTIONs_approx_iso_adps0

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