[English] 日本語
Yorodumi
- PDB-6rmd: Structure of ATP bound Plasmodium falciparum IMP-nucleotidase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rmd
TitleStructure of ATP bound Plasmodium falciparum IMP-nucleotidase
Components(IMP-specific 5'-nucleotidase, putative) x 2
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
ADENOSINE-5'-TRIPHOSPHATE / IMP-specific 5'-nucleotidase 1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 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 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: IMP-specific 5'-nucleotidase, putative
D: IMP-specific 5'-nucleotidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,9896
Polymers94,2952
Non-polymers6934
Water1629
1
A: IMP-specific 5'-nucleotidase, putative
D: IMP-specific 5'-nucleotidase, putative
hetero molecules

A: IMP-specific 5'-nucleotidase, putative
D: IMP-specific 5'-nucleotidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,97812
Polymers188,5914
Non-polymers1,3878
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area14790 Å2
ΔGint-46 kcal/mol
Surface area62000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.690, 210.690, 106.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

-
Components

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


Mass: 50895.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Gene: PF3D7_1206100 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A144A134, 5'-nucleotidase
#2: Protein IMP-specific 5'-nucleotidase, putative


Mass: 43400.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Gene: PF3D7_1206100 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A144A134, 5'-nucleotidase
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.43 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium malonate pH 5.0, 12% (w/v) PEG 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.967 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967 Å / Relative weight: 1
ReflectionResolution: 2.5→47.43 Å / Num. obs: 48313 / % possible obs: 99.9 % / Redundancy: 12.6 % / CC1/2: 1 / Net I/σ(I): 18.4
Reflection shellResolution: 2.5→2.61 Å / Num. unique obs: 5874 / CC1/2: 0.4

-
Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→47.4 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.1
RfactorNum. reflection% reflection
Rfree0.2454 1730 5 %
Rwork0.2002 --
obs0.2025 34611 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6263 0 43 9 6315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056452
X-RAY DIFFRACTIONf_angle_d0.7248759
X-RAY DIFFRACTIONf_dihedral_angle_d11.53874
X-RAY DIFFRACTIONf_chiral_restr0.046990
X-RAY DIFFRACTIONf_plane_restr0.0031115
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.880.3831410.32222681X-RAY DIFFRACTION100
2.88-2.980.34371410.28472674X-RAY DIFFRACTION100
2.98-3.080.32721420.26272701X-RAY DIFFRACTION100
3.08-3.210.32171420.2532711X-RAY DIFFRACTION100
3.21-3.350.33061420.25482695X-RAY DIFFRACTION100
3.35-3.530.22161430.21012716X-RAY DIFFRACTION100
3.53-3.750.25941430.1882712X-RAY DIFFRACTION100
3.75-4.040.24251430.18442720X-RAY DIFFRACTION100
4.04-4.440.20651450.15822752X-RAY DIFFRACTION100
4.44-5.090.1851450.15232764X-RAY DIFFRACTION100
5.09-6.40.26371480.21782798X-RAY DIFFRACTION100
6.41-47.430.23321550.20072957X-RAY DIFFRACTION100
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)
11.65730.8909-0.13171.39480.63531.3043-0.06650.24330.5693-0.0836-0.0947-0.10650.2364-0.06440.13231.12820.046-0.01781.12360.0021.068874.0963-30.0956-0.8757
20.5751-0.3677-0.15455.1443-0.82142.04150.00550.01030.1405-0.4276-0.22480.18950.16610.07580.19610.42690.017-0.04790.56750.09080.479366.1531-36.4197-15.597
31.07050.07460.56282.62730.03193.8690.01770.13660.25-0.3775-0.10480.3146-0.01820.06810.07750.51570.03340.00170.36010.1320.709265.1311-10.6668-6.497
41.99670.17240.44513.1828-0.73612.5859-0.04560.17520.1802-0.5713-0.19350.17590.02310.32490.19580.76930.0628-0.06010.61960.11240.696466.5347-30.0127-19.0682
52.5501-0.6030.14482.5113-0.57962.33370.44750.2458-0.0156-0.6333-0.4776-0.18911.23280.94540.04150.95070.33850.18110.8450.18770.513471.2484-62.8826-1.2948
64.3873-1.41111.34092.9439-1.25493.12060.8183-0.2928-0.8036-0.4276-0.2598-0.11480.7896-0.2159-0.53440.85940.0592-0.14580.55350.15870.698875.7719-82.00822.755
70.42750.18380.75513.49480.59331.3580.3627-0.1224-0.1861-0.0903-0.2608-0.49340.1295-0.0575-0.1280.58630.14980.01670.79730.34310.845286.4389-65.31131.3717
85.1816-1.0867-1.74474.18260.19454.46660.5403-0.452-0.0574-0.3869-0.67780.2485-0.20380.25260.11960.84360.21510.00710.74370.13230.464373.0935-72.31914.0761
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 60 )
2X-RAY DIFFRACTION2chain 'A' and (resid 61 through 211 )
3X-RAY DIFFRACTION3chain 'A' and (resid 212 through 382 )
4X-RAY DIFFRACTION4chain 'A' and (resid 383 through 444 )
5X-RAY DIFFRACTION5chain 'D' and (resid 59 through 144 )
6X-RAY DIFFRACTION6chain 'D' and (resid 145 through 265 )
7X-RAY DIFFRACTION7chain 'D' and (resid 266 through 397 )
8X-RAY DIFFRACTION8chain 'D' and (resid 398 through 430 )

+
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