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- PDB-1inp: CRYSTAL STRUCTURE OF INOSITOL POLYPHOSPHATE 1-PHOSPHATASE AT 2.3 ... -

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Basic information

Entry
Database: PDB / ID: 1inp
TitleCRYSTAL STRUCTURE OF INOSITOL POLYPHOSPHATE 1-PHOSPHATASE AT 2.3 ANGSTROMS RESOLUTION
ComponentsINOSITOL POLYPHOSPHATE 1-PHOSPHATASE
KeywordsHYDROLASE(PHOSPHORIC MONOESTER)
Function / homology
Function and homology information


inositol-1,3,4-trisphosphate 1-phosphatase activity / Synthesis of IP2, IP, and Ins in the cytosol / inositol-1,4-bisphosphate 1-phosphatase / inositol-1,4-bisphosphate 1-phosphatase activity / phosphatidylinositol phosphate biosynthetic process / metal ion binding
Similarity search - Function
Inositol Polyphosphate 1-phosphatase; domain 1 / Inositol Polyphosphate 1-phosphatase, domain 1 / Inositol polyphosphate 1-phosphatase, domain 1 / : / 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 ...Inositol Polyphosphate 1-phosphatase; domain 1 / Inositol Polyphosphate 1-phosphatase, domain 1 / Inositol polyphosphate 1-phosphatase, domain 1 / : / 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 / Few Secondary Structures / Irregular / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Inositol polyphosphate 1-phosphatase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsYork, J.D. / Ponder, J.W. / Chen, Z. / Mathews, F.S. / Majerus, P.W.
Citation
Journal: Biochemistry / Year: 1994
Title: Crystal structure of inositol polyphosphate 1-phosphatase at 2.3-A resolution.
Authors: York, J.D. / Ponder, J.W. / Chen, Z.W. / Mathews, F.S. / Majerus, P.W.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Initial X-Ray Crystallographic Characterization of Recombinant Bovine Inositol Polyphosphate 1-Phosphatase Produced in Spodoptera Frugiperda Cells
Authors: York, J.D. / Chen, Z. / Ponder, J.W. / Chauhan, A.K. / Mathews, F.S. / Majerus, P.W.
History
DepositionOct 4, 1994Processing site: BNL
Revision 1.0Jan 26, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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_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: INOSITOL POLYPHOSPHATE 1-PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,0263
Polymers43,9771
Non-polymers492
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.640, 51.640, 143.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Atom site foot note1: CIS PROLINE - PRO 134
2: LEU 234 - PRO 235 OMEGA = 136.45 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein INOSITOL POLYPHOSPHATE 1-PHOSPHATASE


Mass: 43976.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: BOVINE BRAIN CDNA=20 / Organ: BRAIN / Plasmid: RECOMBINANT DNA/POLYHEDRIN / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P21327, inositol-1,4-bisphosphate 1-phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE STRUCTURE OF 1-PTASE IS SIMILAR TO TWO OTHER MAGNESIUM DEPENDENT/LITHIUM SENSITIVE PHOSPHATASES: ...THE STRUCTURE OF 1-PTASE IS SIMILAR TO TWO OTHER MAGNESIUM DEPENDENT/LITHIUM SENSITIVE PHOSPHATASES: INOSITOL MONO-PHOSPHATE PHOSPHATASE (PDB ENTRY 2HHM) AND FRUCTOSE 1,6-BIS-PHOSPHATASE (PDB ENTRY 1FBP) DESPITE MINIMAL SEQUENCE SIMILARITY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.37 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
113 mg/mlbovine 1-ptase1drop
210 mMbis-Tris1drop
33 mM1dropMgCl2
413 %PEG80001drop
5200 mM1dropLi2SO4
6100 mMTris1drop
713 %PEG80001reservoir
8200 mM1reservoirLi2SO4
9100 mMTris1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 17652 / Observed criterion σ(I): 2
Reflection
*PLUS
Highest resolution: 2.3 Å / % possible obs: 99.3 % / Num. measured all: 63687 / Rmerge F obs: 0.049

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.3→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.198 --
obs0.198 15563 99.3 %
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3773 0 2 210 3985
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.198 / Rfactor Rwork: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 36.28 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d3.6
X-RAY DIFFRACTIONx_dihedral_angle_d26.03
X-RAY DIFFRACTIONx_dihedral_angle_deg

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