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- PDB-6rme: Structure of IMP bound Plasmodium falciparum IMP-nucleotidase mut... -

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Basic information

Entry
Database: PDB / ID: 6rme
TitleStructure of IMP bound Plasmodium falciparum IMP-nucleotidase mutant D172N
Components(IMP-specific 5'-nucleotidase, ...) x 5
KeywordsHYDROLASE / nucleotidase / activator / complex / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


nicotinamide riboside biosynthetic process / nicotinic acid riboside biosynthetic process / inosine salvage / IMP-specific 5'-nucleotidase / IMP 5'-nucleotidase activity / IMP catabolic process / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
IMP-specific 5-nucleotidase / IMP-specific 5'-nucleotidase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
INOSINIC ACID / IMP-specific 5'-nucleotidase 1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsCarrique, L. / Ballut, L. / Violot, S. / Aghajari, N.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-17-CE11-0032 France
CitationJournal: Nat Commun / Year: 2020
Title: Structure and catalytic regulation of Plasmodium falciparum IMP specific nucleotidase.
Authors: Carrique, L. / Ballut, L. / Shukla, A. / Varma, N. / Ravi, R. / Violot, S. / Srinivasan, B. / Ganeshappa, U.T. / Kulkarni, S. / Balaram, H. / Aghajari, N.
History
DepositionMay 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMP-specific 5'-nucleotidase, putative
B: IMP-specific 5'-nucleotidase, putative
C: IMP-specific 5'-nucleotidase, putative
D: IMP-specific 5'-nucleotidase, putative
E: IMP-specific 5'-nucleotidase, putative
F: IMP-specific 5'-nucleotidase, putative
G: IMP-specific 5'-nucleotidase, putative
H: IMP-specific 5'-nucleotidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)365,20126
Polymers362,0368
Non-polymers3,16418
Water543
1
A: IMP-specific 5'-nucleotidase, putative
B: IMP-specific 5'-nucleotidase, putative
C: IMP-specific 5'-nucleotidase, putative
D: IMP-specific 5'-nucleotidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,82213
Polymers181,2404
Non-polymers1,5829
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14090 Å2
ΔGint-107 kcal/mol
Surface area58640 Å2
MethodPISA
2
E: IMP-specific 5'-nucleotidase, putative
F: IMP-specific 5'-nucleotidase, putative
G: IMP-specific 5'-nucleotidase, putative
H: IMP-specific 5'-nucleotidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,37813
Polymers180,7964
Non-polymers1,5829
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13900 Å2
ΔGint-115 kcal/mol
Surface area58920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.260, 204.610, 115.920
Angle α, β, γ (deg.)90.00, 113.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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IMP-specific 5'-nucleotidase, ... , 5 types, 8 molecules AGBDCEHF

#1: Protein IMP-specific 5'-nucleotidase, putative


Mass: 44955.836 Da / Num. of mol.: 2 / Mutation: D172N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Gene: PF3D7_1206100 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A144A134, 5'-nucleotidase
#2: Protein IMP-specific 5'-nucleotidase, putative


Mass: 45083.965 Da / Num. of mol.: 2 / Mutation: D172N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Gene: PF3D7_1206100 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A144A134, 5'-nucleotidase
#3: Protein IMP-specific 5'-nucleotidase, putative


Mass: 46116.172 Da / Num. of mol.: 1 / Mutation: D172N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Gene: PF3D7_1206100 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A144A134, 5'-nucleotidase
#4: Protein IMP-specific 5'-nucleotidase, putative


Mass: 45198.066 Da / Num. of mol.: 2 / Mutation: D172N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Gene: PF3D7_1206100 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A144A134, 5'-nucleotidase
#5: Protein IMP-specific 5'-nucleotidase, putative


Mass: 45444.367 Da / Num. of mol.: 1 / Mutation: D172N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Gene: PF3D7_1206100 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A144A134, 5'-nucleotidase

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Non-polymers , 4 types, 21 molecules

#6: Chemical
ChemComp-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H13N4O8P / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.84 Å3/Da / Density % sol: 56.65 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.5, 0.2 M calcium acetate, 10% (w/v) PEG 8000 , 5 mM IMP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.872 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Oct 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.872 Å / Relative weight: 1
ReflectionResolution: 3.1→47.72 Å / Num. obs: 83738 / % possible obs: 99.7 % / Redundancy: 3.6 % / CC1/2: 0.992 / Net I/σ(I): 6.2
Reflection shellResolution: 3.4→3.6 Å / Num. unique obs: 9981 / CC1/2: 0.548 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RMD

6rmd


Resolution: 3.4→47.25 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 3172 5 %
Rwork0.1964 --
obs0.199 63450 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→47.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23275 0 204 3 23482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00223988
X-RAY DIFFRACTIONf_angle_d0.50332655
X-RAY DIFFRACTIONf_dihedral_angle_d10.9883310
X-RAY DIFFRACTIONf_chiral_restr0.0413754
X-RAY DIFFRACTIONf_plane_restr0.0034131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4-3.450.39691370.31512599X-RAY DIFFRACTION100
3.45-3.50.37111400.29892646X-RAY DIFFRACTION100
3.5-3.560.34781360.27842594X-RAY DIFFRACTION100
3.56-3.620.29321390.26282638X-RAY DIFFRACTION100
3.62-3.690.28971360.24972584X-RAY DIFFRACTION100
3.69-3.760.31531380.24562613X-RAY DIFFRACTION100
3.76-3.840.28681380.22342625X-RAY DIFFRACTION100
3.84-3.920.2911380.22122629X-RAY DIFFRACTION100
3.92-4.010.30071390.21512630X-RAY DIFFRACTION100
4.01-4.110.26861370.19922612X-RAY DIFFRACTION100
4.11-4.220.26331360.19232586X-RAY DIFFRACTION99
4.22-4.350.23171380.18252616X-RAY DIFFRACTION100
4.35-4.490.23511370.1822606X-RAY DIFFRACTION100
4.49-4.650.19671390.16952645X-RAY DIFFRACTION100
4.65-4.830.2231370.16442602X-RAY DIFFRACTION100
4.83-5.050.21671380.16342614X-RAY DIFFRACTION100
5.05-5.320.24461390.17792637X-RAY DIFFRACTION100
5.32-5.650.271370.20912627X-RAY DIFFRACTION100
5.65-6.090.29861390.21732637X-RAY DIFFRACTION100
6.09-6.70.27821390.21572629X-RAY DIFFRACTION100
6.7-7.660.24391380.18712632X-RAY DIFFRACTION99
7.67-9.640.17011390.1462635X-RAY DIFFRACTION99
9.64-47.250.17181380.16512642X-RAY DIFFRACTION99

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