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- PDB-4o7i: Structural and functional characterization of 3'(2'),5'-bisphosph... -

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Basic information

Entry
Database: PDB / ID: 4o7i
TitleStructural and functional characterization of 3'(2'),5'-bisphosphate nucleotidase1 from Entamoeba histolytica
Components3'(2'),5'-bisphosphate nucleotidase, putative
KeywordsHYDROLASE / Li sensitive/Mg dependent Phosphatase / Dephosphorylation
Function / homology
Function and homology information


inositol-1,4-bisphosphate 1-phosphatase / inositol-1,4-bisphosphate 1-phosphatase activity / 3'(2'),5'-bisphosphate nucleotidase / 3'(2'),5'-bisphosphate nucleotidase activity / sulfate assimilation / phosphatidylinositol phosphate biosynthetic process / nucleotide binding / magnesium ion binding / cytoplasm
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 ...: / 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
PHOSPHATE ION / 3',5'-bisphosphate nucleotidase
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsTarique, K.F. / Rehman, S.A.A. / Gourinath, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural elucidation of a dual-activity PAP phosphatase-1 from Entamoeba histolytica capable of hydrolysing both 3'-phosphoadenosine 5'-phosphate and inositol 1,4-bisphosphate
Authors: Faisal Tarique, K. / Arif Abdul Rehman, S. / Gourinath, S.
History
DepositionDec 24, 2013Deposition site: RCSB / Processing site: PDBJ
SupersessionJan 22, 2014ID: 4GDG
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Nov 8, 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.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_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_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: 3'(2'),5'-bisphosphate nucleotidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2733
Polymers36,1541
Non-polymers1192
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.445, 64.520, 117.184
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 3'(2'),5'-bisphosphate nucleotidase, putative


Mass: 36154.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM-1/IMSS / Plasmid: pET28(b) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: C4M4T9, 3'(2'),5'-bisphosphate nucleotidase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.06 Å3/Da / Density % sol: 40.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 28% PEG 4000, 200mM lithium acetate, 5mM magnesium chloride, 5mM adenosine monophospahte, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 17183 / Num. obs: 16255 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 13.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 3.7 / Num. unique all: 1648 / % possible all: 93.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.8.0045refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QGX

1qgx


Resolution: 2.11→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU B: 10.827 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23167 879 5.1 %RANDOM
Rwork0.18434 ---
obs0.1867 15375 95.13 %-
all-16254 --
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.42 Å2
Baniso -1Baniso -2Baniso -3
1--1.87 Å2-0 Å20 Å2
2---0.02 Å20 Å2
3---1.89 Å2
Refine analyzeLuzzati coordinate error obs: 0.2803 Å
Refinement stepCycle: LAST / Resolution: 2.11→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2453 0 6 109 2568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192519
X-RAY DIFFRACTIONr_bond_other_d0.0010.022409
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.973405
X-RAY DIFFRACTIONr_angle_other_deg0.75235569
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3185316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.78125.321109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.86415456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.0041511
X-RAY DIFFRACTIONr_chiral_restr0.0710.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022822
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02534
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4991.5141267
X-RAY DIFFRACTIONr_mcbond_other2.491.5111266
X-RAY DIFFRACTIONr_mcangle_it3.2242.2551582
X-RAY DIFFRACTIONr_mcangle_other3.2272.2581583
X-RAY DIFFRACTIONr_scbond_it5.0932.0381252
X-RAY DIFFRACTIONr_scbond_other5.0922.0421253
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2682.8891824
X-RAY DIFFRACTIONr_long_range_B_refined7.15813.5972855
X-RAY DIFFRACTIONr_long_range_B_other7.16113.5062828
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.105→2.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 80 -
Rwork0.227 1092 -
obs--89.74 %
Refinement TLS params.Method: refined / Origin x: 22.641 Å / Origin y: 36.2 Å / Origin z: 17.06 Å
111213212223313233
T0.0386 Å20.0101 Å20.0023 Å2-0.0047 Å20.0042 Å2--0.0332 Å2
L0.4351 °20.185 °2-0.066 °2-0.9203 °20.0679 °2--1.2928 °2
S0.0079 Å °0.0112 Å °-0.0254 Å °0.0106 Å °0.0001 Å °-0.0674 Å °0.0934 Å °0.0546 Å °-0.008 Å °

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