[English] 日本語
Yorodumi
- PDB-6agy: Aspergillus fumigatus Af293 NDK -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6agy
TitleAspergillus fumigatus Af293 NDK
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / Kinase
Function / homology
Function and homology information


nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / nucleoside diphosphate kinase activity / GTP biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits ...Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesAspergillus fumigatus Af293 (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHu, Y. / Han, L.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: Characterization of crystal structure and key residues of Aspergillus fumigatus nucleoside diphosphate kinase.
Authors: Hu, Y. / Jia, X. / Lu, Z. / Han, L.
History
DepositionAug 15, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)18,0241
Polymers18,0241
Non-polymers00
Water3,315184
1
A: Nucleoside diphosphate kinase
x 6


Theoretical massNumber of molelcules
Total (without water)108,1426
Polymers108,1426
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation4_665-y+1,-x+1,-z1
crystal symmetry operation5_555-x+y,y,-z1
crystal symmetry operation6_565x,x-y+1,-z1
Buried area15250 Å2
ΔGint-86 kcal/mol
Surface area32970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.756, 70.756, 53.095
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number149
Space group name H-MP312
Components on special symmetry positions
IDModelComponents
11A-266-

HOH

21A-356-

HOH

31A-372-

HOH

-
Components

#1: Protein Nucleoside diphosphate kinase / NDP kinase


Mass: 18023.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus Af293 (mold) / Strain: Af293 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z8P9, nucleoside-diphosphate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.22 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.8 / Details: 0.1M HEPES pH 6.8, 1.2M sodium citrate

-
Data collection

DiffractionMean temperature: 180 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.542 Å
DetectorType: RAYONIX SX-165mm / Detector: CCD / Date: Jun 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 14227 / % possible obs: 97.67 % / Redundancy: 10.8 % / Biso Wilson estimate: 14.65 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07438 / Rpim(I) all: 0.02362 / Rrim(I) all: 0.07809 / Net I/σ(I): 26.57
Reflection shellResolution: 1.8→1.864 Å / Redundancy: 10.5 % / Rmerge(I) obs: 0.4399 / Mean I/σ(I) obs: 5.08 / Num. unique obs: 1406 / CC1/2: 0.948 / Rpim(I) all: 0.1416 / Rrim(I) all: 0.4623 / % possible all: 94.1

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FKX

4fkx


Resolution: 1.8→26.547 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 14.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1702 1400 10.05 %
Rwork0.1374 --
obs0.1407 13936 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→26.547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1161 0 0 184 1345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051190
X-RAY DIFFRACTIONf_angle_d0.7991612
X-RAY DIFFRACTIONf_dihedral_angle_d8.968708
X-RAY DIFFRACTIONf_chiral_restr0.051175
X-RAY DIFFRACTIONf_plane_restr0.005207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7998-1.86410.1981380.15461193X-RAY DIFFRACTION94
1.8641-1.93870.2061370.13961200X-RAY DIFFRACTION95
1.9387-2.02690.16871390.12151249X-RAY DIFFRACTION98
2.0269-2.13370.1861380.12841239X-RAY DIFFRACTION98
2.1337-2.26740.16571390.12781256X-RAY DIFFRACTION98
2.2674-2.44230.16651390.12491252X-RAY DIFFRACTION98
2.4423-2.68790.16911430.13491268X-RAY DIFFRACTION99
2.6879-3.07630.18951380.14231287X-RAY DIFFRACTION99
3.0763-3.87390.14671430.12931285X-RAY DIFFRACTION100
3.8739-26.55040.16461460.15621307X-RAY DIFFRACTION98

+
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