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- PDB-3n9v: Crystal Structure of INPP5B -

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Basic information

Entry
Database: PDB / ID: 3n9v
TitleCrystal Structure of INPP5B
ComponentsType II inositol-1,4,5-trisphosphate 5-phosphatase
KeywordsHYDROLASE / INPP5B / Phosphoinositide 5-phosphatase / inositol signalling / phosphatase / magnesium / structural genomics / SGC / SGC Stockholm / Structural Genomics Consortium
Function / homology
Function and homology information


Synthesis of IP2, IP, and Ins in the cytosol / inositol phosphate metabolic process / flagellated sperm motility / inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity / inositol-1,4,5-trisphosphate 5-phosphatase activity / phosphoinositide 5-phosphatase / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol dephosphorylation / regulation of protein processing / Synthesis of IP3 and IP4 in the cytosol ...Synthesis of IP2, IP, and Ins in the cytosol / inositol phosphate metabolic process / flagellated sperm motility / inositol-1,3,4,5-tetrakisphosphate 5-phosphatase activity / inositol-1,4,5-trisphosphate 5-phosphatase activity / phosphoinositide 5-phosphatase / phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity / phosphatidylinositol dephosphorylation / regulation of protein processing / Synthesis of IP3 and IP4 in the cytosol / endoplasmic reticulum-Golgi intermediate compartment / phagocytic vesicle membrane / early endosome membrane / spermatogenesis / in utero embryonic development / Golgi apparatus / signal transduction / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
INPP5B, PH domain / Type II inositol 1,4,5-trisphosphate 5-phosphatase PH domain / : / : / Inositol polyphosphate 5-phosphatase OCRL-like, ASH domain / OCRL1/INPP5B, INPP5c domain / : / Inositol polyphosphate-related phosphatase / Inositol polyphosphate phosphatase, catalytic domain homologues / Deoxyribonuclease I; Chain A ...INPP5B, PH domain / Type II inositol 1,4,5-trisphosphate 5-phosphatase PH domain / : / : / Inositol polyphosphate 5-phosphatase OCRL-like, ASH domain / OCRL1/INPP5B, INPP5c domain / : / Inositol polyphosphate-related phosphatase / Inositol polyphosphate phosphatase, catalytic domain homologues / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Endonuclease/exonuclease/phosphatase superfamily / Rho GTPase activation protein / 4-Layer Sandwich / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
Type II inositol 1,4,5-trisphosphate 5-phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsTresaugues, L. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Tresaugues, L. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kol, S. / Kotenyova, T. / Moche, M. / Nyman, T. / Persson, C. / Schuler, H. / Schutz, P. / Siponen, M.I. / Thorsell, A.G. / van der Berg, S. / Wahlberg, E. / Weigelt, J. / Wisniewska, M. / Nordlund, P. / Structural Genomics Consortium (SGC)
CitationJournal: Structure / Year: 2014
Title: Structural basis for phosphoinositide substrate recognition, catalysis, and membrane interactions in human inositol polyphosphate 5-phosphatases
Authors: Tresaugues, L. / Silvander, C. / Flodin, S. / Welin, M. / Nyman, T. / Graslund, S. / Hammarstrom, M. / Berglund, H. / Nordlund, P.
History
DepositionMay 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 28, 2014Group: Database references
Revision 1.3Sep 6, 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_conn_angle / struct_conn / 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 / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Type II inositol-1,4,5-trisphosphate 5-phosphatase
B: Type II inositol-1,4,5-trisphosphate 5-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4857
Polymers72,2642
Non-polymers2215
Water1,02757
1
A: Type II inositol-1,4,5-trisphosphate 5-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2884
Polymers36,1321
Non-polymers1563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Type II inositol-1,4,5-trisphosphate 5-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1963
Polymers36,1321
Non-polymers642
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.160, 110.660, 159.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121

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Components

#1: Protein Type II inositol-1,4,5-trisphosphate 5-phosphatase / Phosphoinositide 5-phosphatase / 5PTase / 75 kDa inositol polyphosphate-5-phosphatase


Mass: 36131.945 Da / Num. of mol.: 2 / Fragment: UNP residues 342-647
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INPP5B / Plasmid: pNIC-CH2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) R3 pRARE / References: UniProt: P32019, phosphoinositide 5-phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.93 Å3/Da / Density % sol: 58.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Magnesium Chloride, 0.1M Tris-HCl pH 8.5, 20% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9686 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 23, 2009 / Details: mirrors
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.6→72.548 Å / Num. all: 25087 / Num. obs: 25062 / % possible obs: 99.9 % / Redundancy: 4.6 % / Biso Wilson estimate: 79.4 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 11.9
Reflection shellResolution: 2.6→2.793 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3602 / Rsym value: 0.62 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I9Y

1i9y


Resolution: 2.65→53.661 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 1146 4.58 %RANDOM
Rwork0.1896 ---
obs0.1914 25049 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.562 Å2 / ksol: 0.339 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.1499 Å2-0 Å2-0 Å2
2---0.4532 Å20 Å2
3----9.6967 Å2
Refinement stepCycle: LAST / Resolution: 2.65→53.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4645 0 10 57 4712
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114763
X-RAY DIFFRACTIONf_angle_d1.2576458
X-RAY DIFFRACTIONf_dihedral_angle_d17.6331655
X-RAY DIFFRACTIONf_chiral_restr0.076703
X-RAY DIFFRACTIONf_plane_restr0.005829
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.77060.33111490.26312935X-RAY DIFFRACTION100
2.7706-2.91670.26761300.23582971X-RAY DIFFRACTION100
2.9167-3.09940.2881450.21932953X-RAY DIFFRACTION100
3.0994-3.33870.26291500.19092952X-RAY DIFFRACTION100
3.3387-3.67460.21641490.17712954X-RAY DIFFRACTION100
3.6746-4.20610.19661520.16092975X-RAY DIFFRACTION100
4.2061-5.29860.16881390.14293031X-RAY DIFFRACTION100
5.2986-53.67250.25821320.20753132X-RAY DIFFRACTION99
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)
11.6127-1.0010.61761.6215-0.18281.64760.07230.11840.09650.0560.07920.2434-0.3385-0.3772-00.42290.03520.05730.44870.05780.4631-22.8689-6.347-20.3111
22.076-0.0259-0.67683.0809-0.65352.18620.05840.2461-0.1377-0.3570.0850.32830.3266-0.154800.3273-0.0105-0.02870.32040.02890.2865-21.997-17.7784-25.6651
32.0871-0.58970.68032.0725-0.04052.71750.04750.11940.16980.05580.0594-0.2166-0.02490.0267-00.6137-0.0028-0.04620.4865-0.04180.54668.7149-6.2028-18.154
41.6045-0.38481.87051.5881-0.22.5961-0.1664-0.0020.60960.5960.0289-0.4107-1.18580.403400.8021-0.2399-0.10630.5351-0.02160.820917.05557.8626-18.263
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 261:328)
2X-RAY DIFFRACTION2(chain A and resid 329:563)
3X-RAY DIFFRACTION3(chain B and resid 261:404)
4X-RAY DIFFRACTION4(chain B and resid 405:562)

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