[English] 日本語
Yorodumi
- PDB-6awj: Staphylococcus aureus Type II pantothenate kinase in complex with... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6awj
TitleStaphylococcus aureus Type II pantothenate kinase in complex with ADP and pantothenate analog Deoxy-MeO-N5Pan with pantothenate present in reaction
ComponentsType II pantothenate kinase
KeywordsTRANSFERASE / Staphylococcus aureus / SaPanK / ADP / pantothenate analog
Function / homology
Function and homology information


pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / ATP binding / cytosol
Similarity search - Function
Type II pantothenate kinase, bacterial / Fumble / Type II pantothenate kinase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-N7G / Type II pantothenate kinase / Type II pantothenate kinase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChen, Y. / Antoshchenko, T. / Strauss, E. / Barnard, L. / Huang, Y.H.
CitationJournal: To Be Published
Title: Structure-based identification of uncompetitive inhibitors for Staphylococcus aureus pantothenate kinase.
Authors: Chen, Y. / Antoshchenko, T. / Strauss, E. / Barnard, L. / Huang, Y.H.
History
DepositionSep 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Type II pantothenate kinase
B: Type II pantothenate kinase
C: Type II pantothenate kinase
D: Type II pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,91012
Polymers115,9914
Non-polymers2,9188
Water2,792155
1
A: Type II pantothenate kinase
B: Type II pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4556
Polymers57,9962
Non-polymers1,4594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-54 kcal/mol
Surface area20940 Å2
MethodPISA
2
C: Type II pantothenate kinase
D: Type II pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4556
Polymers57,9962
Non-polymers1,4594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6630 Å2
ΔGint-53 kcal/mol
Surface area20700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.242, 57.285, 133.751
Angle α, β, γ (deg.)90.000, 99.840, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Type II pantothenate kinase / PanK-II / Pantothenic acid kinase


Mass: 28997.770 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria)
Gene: coaW, AYM28_11860, AYM37_11860, ERS072738_01917, ERS074020_01878, HMPREF3211_02599
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0D6HHM8, UniProt: Q2FWC7*PLUS, pantothenate kinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-N7G / (2R)-2-hydroxy-N-{3-[(5-methoxypentyl)amino]-3-oxopropyl}-3,3-dimethylbutanamide


Mass: 302.410 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H30N2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG3350, 0.2 M lithium sulfate, 0.1 M Bis-Tris, pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 30, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.5→132 Å / Num. obs: 38162 / % possible obs: 99.7 % / Redundancy: 3.54 % / Net I/σ(I): 7.75
Reflection shellHighest resolution: 2.5 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.884 / SU B: 13.972 / SU ML: 0.301 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.111 / ESU R Free: 0.327
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1912 5 %RANDOM
Rwork0.2256 ---
obs0.2276 36241 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 115.22 Å2 / Biso mean: 35.878 Å2 / Biso min: 2.75 Å2
Baniso -1Baniso -2Baniso -3
1-2.42 Å20 Å2-3.47 Å2
2---1.46 Å2-0 Å2
3---0.24 Å2
Refinement stepCycle: final / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8095 0 192 155 8442
Biso mean--25.21 30.8 -
Num. residues----1056
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0198429
X-RAY DIFFRACTIONr_bond_other_d0.0080.028088
X-RAY DIFFRACTIONr_angle_refined_deg1.7031.97211433
X-RAY DIFFRACTIONr_angle_other_deg1.5883.00518538
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04551050
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.48625.263380
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.768151383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8631532
X-RAY DIFFRACTIONr_chiral_restr0.0940.21304
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029616
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021928
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 132 -
Rwork0.323 2637 -
all-2769 -
obs--98.96 %

+
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