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- PDB-6rmw: Structure of N-terminal truncated IMP bound Plasmodium falciparum... -

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Basic information

Entry
Database: PDB / ID: 6rmw
TitleStructure of N-terminal truncated IMP bound Plasmodium falciparum IMP-nucleotidase
ComponentsIMP-specific 5'-nucleotidase, putative
KeywordsHYDROLASE / nucleotidase / activator / complex
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 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 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 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 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)391,13926
Polymers387,9758
Non-polymers3,16418
Water0
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)195,56913
Polymers193,9874
Non-polymers1,5829
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14320 Å2
ΔGint-111 kcal/mol
Surface area59110 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)195,56913
Polymers193,9874
Non-polymers1,5829
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13980 Å2
ΔGint-113 kcal/mol
Surface area59210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.800, 203.900, 115.300
Angle α, β, γ (deg.)90.00, 113.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 48496.832 Da / Num. of mol.: 8 / Mutation: D172N
Source method: isolated from a genetically manipulated source
Details: First 30 residues are truncated in the construction which also contains the mutation D172N
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF3D7_1206100 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A144A134, 5'-nucleotidase
#2: Chemical
ChemComp-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: 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
Has ligand of interestN

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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: 3 Å3/Da / Density % sol: 58.97 %
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 by co-crystallizing the protein with 5 mM of IMP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→49.7 Å / Num. obs: 57015 / % possible obs: 99.14 % / Redundancy: 6.7 % / CC1/2: 0.76 / Net I/σ(I): 4.2
Reflection shellResolution: 3.5→4.3 Å / Num. unique obs: 26211 / CC1/2: 0.767

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RMD

6rmd


Resolution: 3.5→48.073 Å / SU ML: 0.77 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.279 2851 5 %
Rwork0.2364 --
obs0.2386 56981 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→48.073 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23414 0 204 0 23618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00224126
X-RAY DIFFRACTIONf_angle_d0.45132811
X-RAY DIFFRACTIONf_dihedral_angle_d4.81114304
X-RAY DIFFRACTIONf_chiral_restr0.0393755
X-RAY DIFFRACTIONf_plane_restr0.0034152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.56040.42111390.41152639X-RAY DIFFRACTION99
3.5604-3.62510.41351430.39032726X-RAY DIFFRACTION100
3.6251-3.69480.37331420.37472691X-RAY DIFFRACTION100
3.6948-3.77020.37711440.34852728X-RAY DIFFRACTION100
3.7702-3.85210.37611450.33732759X-RAY DIFFRACTION99
3.8521-3.94170.3541410.3132690X-RAY DIFFRACTION100
3.9417-4.04020.35291420.30052683X-RAY DIFFRACTION99
4.0402-4.14940.35291400.28412659X-RAY DIFFRACTION97
4.1494-4.27140.31181440.27332734X-RAY DIFFRACTION100
4.2714-4.40920.34611420.26762700X-RAY DIFFRACTION100
4.4092-4.56670.34591420.25452713X-RAY DIFFRACTION100
4.5667-4.74940.26511440.23422717X-RAY DIFFRACTION100
4.7494-4.96530.28341420.23052712X-RAY DIFFRACTION99
4.9653-5.22680.2541420.22242686X-RAY DIFFRACTION98
5.2268-5.55380.33211430.2442721X-RAY DIFFRACTION100
5.5538-5.98190.32931430.26262715X-RAY DIFFRACTION100
5.9819-6.58250.27671430.24562718X-RAY DIFFRACTION99
6.5825-7.53190.22971420.21562697X-RAY DIFFRACTION98
7.5319-9.47740.21911440.1682745X-RAY DIFFRACTION99

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