[English] 日本語
Yorodumi
- PDB-6rmw: Structure of N-terminal truncated IMP bound Plasmodium falciparum... -

+
Open data


ID or keywords:

Loading...

-
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 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
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)391,13926
Polymers387,9758
Non-polymers3,16418
Water00
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

-
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


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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