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- PDB-4qxd: Crystal structure of Inositol Polyphosphate 1-Phosphatase from En... -

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Basic information

Entry
Database: PDB / ID: 4qxd
TitleCrystal structure of Inositol Polyphosphate 1-Phosphatase from Entamoeba histolytica
Components3'(2'),5'-bisphosphate nucleotidase, putative
KeywordsHYDROLASE / 1D-myo-inositol 1 / 4-bisphosphate / Hydrolysis / 1D-myo-inositol 4-phosphate / phosphate
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 / magnesium ion binding / cytoplasm
Similarity search - Function
: / 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 / Inositol polyphosphate 1-phosphatase
Similarity search - Component
Biological speciesEntamoeba histolytica HM-1:IMSS (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsTarique, K.F. / Abdul Rehman, S.A. / Betzel, C. / Gourinath, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure-based identification of inositol polyphosphate 1-phosphatase from Entamoeba histolytica
Authors: Tarique, K.F. / Abdul Rehman, S.A. / Betzel, C. / Gourinath, S.
History
DepositionJul 19, 2014Deposition site: RCSB / Processing site: PDBJ
SupersessionAug 6, 2014ID: 4J13
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
B: 3'(2'),5'-bisphosphate nucleotidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,64410
Polymers66,3082
Non-polymers3368
Water50428
1
A: 3'(2'),5'-bisphosphate nucleotidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3225
Polymers33,1541
Non-polymers1684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 3'(2'),5'-bisphosphate nucleotidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3225
Polymers33,1541
Non-polymers1684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.741, 76.289, 101.067
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 1 - 287 / Label seq-ID: 1 - 287

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein 3'(2'),5'-bisphosphate nucleotidase, putative / Inositol Polyphosphate 1-Phosphatase


Mass: 33154.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica HM-1:IMSS (eukaryote)
Gene: EHI_179820 / Plasmid: pET(28b) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: C4M633, inositol-1,4-bisphosphate 1-phosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 12.5% MPD, 12.5% Peg 1k, 12.5% Peg 3350, 0.03M salt mixture, pH 6.7, 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: 1.5417 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 19012 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.1 % / Rsym value: 0.1 / Net I/σ(I): 24.29
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 11.6 % / Mean I/σ(I) obs: 4.32 / Num. unique all: 1876 / Rsym value: 0.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Model obtained from low resolution anomalous data

Resolution: 2.55→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.916 / SU B: 23.695 / SU ML: 0.238 / Cross valid method: THROUGHOUT / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24954 975 5.1 %RANDOM
Rwork0.19291 ---
obs0.19573 17989 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.583 Å2
Baniso -1Baniso -2Baniso -3
1-2.02 Å20 Å2-0 Å2
2---2.92 Å2-0 Å2
3---0.89 Å2
Refine analyzeLuzzati coordinate error obs: 0.3923 Å
Refinement stepCycle: LAST / Resolution: 2.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4566 0 16 28 4610
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194669
X-RAY DIFFRACTIONr_bond_other_d0.0030.024520
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.9756325
X-RAY DIFFRACTIONr_angle_other_deg0.828310486
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2095575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.08926.073191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.39115863
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.312154
X-RAY DIFFRACTIONr_chiral_restr0.0630.2725
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215165
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02969
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_it1.572.9972306
X-RAY DIFFRACTIONr_mcbond_other1.572.9972305
X-RAY DIFFRACTIONr_mcangle_it2.5094.4952879
X-RAY DIFFRACTIONr_mcangle_other2.5094.4952880
X-RAY DIFFRACTIONr_scbond_it2.0523.2462363
X-RAY DIFFRACTIONr_scbond_other2.0373.2442360
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2734.7523441
X-RAY DIFFRACTIONr_long_range_B_refined4.70823.8555181
X-RAY DIFFRACTIONr_long_range_B_other4.70423.8415177
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 17971 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.547→2.613 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 70 -
Rwork0.25 1296 -
obs--98.84 %
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)
11.434-0.5059-0.22032.8688-0.08023.69530.08140.04670.06650.0009-0.05010.1228-0.3268-0.2604-0.03130.06970.0227-0.00190.0562-0.02050.026213.06810.9355.942
21.0973-0.43740.02392.58520.43433.49310.10.0472-0.0915-0.37090.006-0.04660.180.2564-0.1060.1716-0.0147-0.02410.07630.00190.0181-15.283-10.8734.12
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 288
2X-RAY DIFFRACTION2B1 - 289

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