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- PDB-1jp4: Crystal Structure of an Enzyme Displaying both Inositol-Polyphosp... -

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Basic information

Entry
Database: PDB / ID: 1jp4
TitleCrystal Structure of an Enzyme Displaying both Inositol-Polyphosphate 1-Phosphatase and 3'-Phosphoadenosine-5'-Phosphate Phosphatase Activities
Components3'(2'),5'-bisphosphate nucleotidase
KeywordsHYDROLASE / protein-product complex / sugar nucleotidase fold
Function / homology
Function and homology information


Cytosolic sulfonation of small molecules / inositol-1,4-bisphosphate 1-phosphatase activity / 3'(2'),5'-bisphosphate nucleotidase / 3'(2'),5'-bisphosphate nucleotidase activity / : / phosphatidylinositol phosphate biosynthetic process / magnesium ion binding
Similarity search - Function
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 ...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
ADENOSINE MONOPHOSPHATE / BETA-MERCAPTOETHANOL / PHOSPHATE ION / 3'(2'),5'-bisphosphate nucleotidase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.69 Å
AuthorsPatel, S. / Yenush, L. / Rodriguez, P.L. / Serrano, R. / Blundell, T.L.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Crystal structure of an enzyme displaying both inositol-polyphosphate-1-phosphatase and 3'-phosphoadenosine-5'-phosphate phosphatase activities: a novel target of lithium therapy.
Authors: Patel, S. / Yenush, L. / Rodriguez, P.L. / Serrano, R. / Blundell, T.L.
History
DepositionAug 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_src_syn / 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 / _entity.details / _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_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_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.pdbx_leaving_atom_flag / _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: 3'(2'),5'-bisphosphate nucleotidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8027
Polymers33,2091
Non-polymers5936
Water7,530418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.635, 74.493, 92.827
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 3'(2'),5'-bisphosphate nucleotidase / PIPase: PAP and Inositol 1 / 4 bisphosphate Phosphatase


Mass: 33208.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Sal3 / Plasmid: pET24a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3
References: UniProt: Q9Z1N4, 3'(2'),5'-bisphosphate nucleotidase, inositol-1,4-bisphosphate 1-phosphatase

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Non-polymers , 5 types, 424 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
Details: AMP came from PAP (Sigma-Aldrich) turnover by enzyme
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
Details: inorganic phosphate came from PAP (sigma-Aldrich) turnover by enzyme
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Details: Magnesium ions came from crystallisation buffer / Comment: AMP*YM
#5: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Details: BME came from protein purification buffer
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8K, magnesium acetate, sodium cacodylate, lithium chloride, magnesium chloride, PAP, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 %(w/v)PEG80001reservoir
20.2 Mmagnesium acetate1reservoir
30.1 Msodium cacodylate1reservoirpH6.5
410 mg/mlprotein1drop
55 mM1dropMgCl2
66 mM1dropLi2SO4
70.6 mMPAP1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSRS PX9.611.244
SYNCHROTRONESRF BM1420.97911, 0.97923, 0.91847
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDApr 20, 2000
MARRESEARCH2CCDJun 26, 2000
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(III) monochromatorSINGLE WAVELENGTHMx-ray1
2Si(III) monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.2441
20.979111
30.979231
40.918471
ReflectionResolution: 1.69→24.94 Å / Num. all: 38295 / Num. obs: 38295 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 12.4
Reflection shellResolution: 1.69→1.78 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 4 / Num. unique all: 5441 / Rsym value: 0.369 / % possible all: 99.6
Reflection
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
% possible obs: 99.6 %

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Processing

Software
NameVersionClassification
SnBv2.0phasing
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.69→24.94 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.274 / SU ML: 0.076 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.083 / ESU R Free: 0.085 / Stereochemistry target values: Engh & Huber
Details: Structure was initially solved by ARP/wARP automated backbone tracing facility.
RfactorNum. reflection% reflectionSelection details
Rfree0.18016 1918 5 %RANDOM
Rwork0.14696 ---
all0.14866 38295 --
obs0.14866 38295 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.832 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2--0.47 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.69→24.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2269 0 35 424 2728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222337
X-RAY DIFFRACTIONr_bond_other_d00.022149
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.9813174
X-RAY DIFFRACTIONr_angle_other_deg1.9435019
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6033300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.33315423
X-RAY DIFFRACTIONr_chiral_restr0.1110.2368
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022574
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02415
X-RAY DIFFRACTIONr_nbd_refined0.2360.3470
X-RAY DIFFRACTIONr_nbd_other0.1950.32033
X-RAY DIFFRACTIONr_nbtor_other0.1990.52
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2350.5293
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0680.35
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1740.328
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.530
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.4961.51494
X-RAY DIFFRACTIONr_mcangle_it2.35422404
X-RAY DIFFRACTIONr_scbond_it3.2453843
X-RAY DIFFRACTIONr_scangle_it4.6874.5770
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.69→1.78 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 --
Rwork0.19 --
obs-5541 99.6 %
Software
*PLUS
Name: REFMAC / Version: 5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 57.7 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.147 / Rfactor Rfree: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.67
X-RAY DIFFRACTIONp_plane_restr0.007
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it
LS refinement shell
*PLUS
Lowest resolution: 1.77 Å / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.19

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