[English] 日本語
Yorodumi
- PDB-7mk0: Trypanosoma cruzi Nucleoside Diphosphate Kinase 1 form a quinary ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mk0
TitleTrypanosoma cruzi Nucleoside Diphosphate Kinase 1 form a quinary multihexameric structure
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / Kinase / cruzi / ndpk1
Function / homology
Function and homology information


nucleoside-diphosphate kinase / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / ATP binding
Similarity search - Function
Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily
Similarity search - Domain/homology
Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsGomez, J.A. / Aguilar, C.F.
Funding support Brazil, Argentina, 2items
OrganizationGrant numberCountry
Coordination for the Improvement of Higher Education Personnel Brazil
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT) Argentina
Citation
Journal: Acta Crystallogr D Struct Biol / Year: 2022
Title: X-ray diffraction and in vivo studies reveal the quinary structure of Trypanosoma cruzi nucleoside diphosphate kinase 1: a novel helical oligomer structure.
Authors: Gomez Barroso, J.A. / Miranda, M.R. / Pereira, C.A. / Garratt, R.C. / Aguilar, C.F.
#1: Journal: Acta Crystallographica Section F Structural Biology and Crystallization Communications
Year: 2010
Title: Protein preparation, crystallization and preliminary X-ray analysis of Trypanosoma cruzi nucleoside diphosphate kinase 1
Authors: Gomez, J.A. / Aguilar, C.F.
History
DepositionApr 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
E: Nucleoside diphosphate kinase
F: Nucleoside diphosphate kinase
G: Nucleoside diphosphate kinase
H: Nucleoside diphosphate kinase
I: Nucleoside diphosphate kinase
J: Nucleoside diphosphate kinase
K: Nucleoside diphosphate kinase
L: Nucleoside diphosphate kinase
M: Nucleoside diphosphate kinase
N: Nucleoside diphosphate kinase
O: Nucleoside diphosphate kinase
P: Nucleoside diphosphate kinase
Q: Nucleoside diphosphate kinase
R: Nucleoside diphosphate kinase
S: Nucleoside diphosphate kinase
T: Nucleoside diphosphate kinase
U: Nucleoside diphosphate kinase
V: Nucleoside diphosphate kinase
W: Nucleoside diphosphate kinase
X: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)401,81224
Polymers401,81224
Non-polymers00
Water00
1
A: Nucleoside diphosphate kinase
B: Nucleoside diphosphate kinase
C: Nucleoside diphosphate kinase
D: Nucleoside diphosphate kinase
E: Nucleoside diphosphate kinase
F: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)100,4536
Polymers100,4536
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15550 Å2
ΔGint-68 kcal/mol
Surface area35480 Å2
MethodPISA
2
G: Nucleoside diphosphate kinase
H: Nucleoside diphosphate kinase
I: Nucleoside diphosphate kinase
J: Nucleoside diphosphate kinase
K: Nucleoside diphosphate kinase
L: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)100,4536
Polymers100,4536
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16680 Å2
ΔGint-72 kcal/mol
Surface area34570 Å2
MethodPISA
3
M: Nucleoside diphosphate kinase
N: Nucleoside diphosphate kinase
O: Nucleoside diphosphate kinase
P: Nucleoside diphosphate kinase
Q: Nucleoside diphosphate kinase
R: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)100,4536
Polymers100,4536
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16170 Å2
ΔGint-73 kcal/mol
Surface area35590 Å2
MethodPISA
4
S: Nucleoside diphosphate kinase
T: Nucleoside diphosphate kinase
U: Nucleoside diphosphate kinase
V: Nucleoside diphosphate kinase
W: Nucleoside diphosphate kinase
X: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)100,4536
Polymers100,4536
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16220 Å2
ΔGint-76 kcal/mol
Surface area35200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.842, 127.842, 275.494
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3

-
Components

#1: Protein ...
Nucleoside diphosphate kinase


Mass: 16742.168 Da / Num. of mol.: 24
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: C3747_234g48, C3747_68g44, C4B63_80g21 / Plasmid: pRSET-A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A2V2WVR0, nucleoside-diphosphate kinase

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 61.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: PEG3350 20% Magnesium chloride 200mM

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.45 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 30, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.291
11-K, -H, -L20.237
11K, H, -L30.24
11-h,-k,l40.232
ReflectionResolution: 3→86.38 Å / Num. obs: 58612 / % possible obs: 92.3 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.34 / Net I/σ(I): 2.7
Reflection shellResolution: 3.498→3.69 Å / Rmerge(I) obs: 1.121 / Num. unique obs: 9287 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
SCALA5.6.0117data scaling
REFMAC5.6.0117refinement
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BBC

3bbc


Resolution: 3.5→10 Å / Cor.coef. Fo:Fc: 0.432 / Cor.coef. Fo:Fc free: 0.387 / SU B: 11.722 / SU ML: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2777 3266 5.4 %RANDOM
Rwork0.2686 ---
obs0.2691 57214 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 275.14 Å2 / Biso mean: 15.659 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-2.76 Å20 Å20 Å2
2--2.76 Å20 Å2
3----5.52 Å2
Refinement stepCycle: final / Resolution: 3.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28296 0 0 0 28296
Num. residues----3624
LS refinement shellResolution: 3.5→3.577 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.227 254 -
Rwork0.192 3794 -
obs--96.68 %

+
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://pdbjlvh1.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