[English] 日本語
Yorodumi
- PDB-6rme: Structure of IMP bound Plasmodium falciparum IMP-nucleotidase mut... -

+
Open data


ID or keywords:

Loading...

-
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 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
Revision 1.2Oct 1, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact ...pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
Non-polymers , 4 types, 21 molecules

#6: Chemical
ChemComp-IMP / 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


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


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

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more