[English] 日本語
Yorodumi
- PDB-5xlw: Mycobacterium tuberculosis Pantothenate kinase mutant F247A/F254A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5xlw
TitleMycobacterium tuberculosis Pantothenate kinase mutant F247A/F254A
ComponentsPantothenate kinase
KeywordsTRANSFERASE / Homodimer / CoA biosynthesis / Nucleotide binding / Concerted movement / Structural transformation
Function / homology
Function and homology information


pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / phosphorylation / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Pantothenate kinase / Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Pantothenate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsPaul, A. / Kumar, P. / Surolia, A. / Vijayan, M.
Citation
Journal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Biochemical and structural studies of mutants indicate concerted movement of the dimer interface and ligand-binding region of Mycobacterium tuberculosis pantothenate kinase
Authors: Paul, A. / Kumar, P. / Surolia, A. / Vijayan, M.
#1: Journal: Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun.
Year: 2005
Title: Expression, purification, crystallization and preliminary X-ray crystallographic analysis of pantothenate kinase from Mycobacterium tuberculosis.
Authors: Das, S. / Kumar, P. / Bhor, V. / Surolia, A. / Vijayan, M.
#2: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2006
Title: Invariance and variability in bacterial PanK: a study based on the crystal structure of Mycobacterium tuberculosis PanK.
Authors: Das, S. / Kumar, P. / Bhor, V. / Surolia, A. / Vijayan, M.
#3: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2009
Title: Mycobacterium tuberculosis pantothenate kinase: possible changes in location of ligands during enzyme action.
Authors: Chetnani, B. / Das, S. / Kumar, P. / Surolia, A. / Vijayan, M.
#4: Journal: J. Mol. Biol. / Year: 2010
Title: M. tuberculosis pantothenate kinase: dual substrate specificity and unusual changes in ligand locations.
Authors: Chetnani, B. / Kumar, P. / Surolia, A. / Vijayan, M.
#5: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2011
Title: Location and conformation of pantothenate and its derivatives in Mycobacterium tuberculosis pantothenate kinase: insights into enzyme action.
Authors: Chetnani, B. / Kumar, P. / Abhinav, K.V. / Chhibber, M. / Surolia, A. / Vijayan, M.
History
DepositionMay 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 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
B: Pantothenate kinase
A: Pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,07528
Polymers71,1052
Non-polymers1,97026
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10190 Å2
ΔGint-50 kcal/mol
Surface area25170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.330, 119.330, 127.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

-
Protein , 1 types, 2 molecules BA

#1: Protein Pantothenate kinase / Pantothenic acid kinase


Mass: 35552.660 Da / Num. of mol.: 2 / Mutation: F247A, F254A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: coaA, Rv1092c, MTV017.45c / Plasmid: Pet28a(+) / Details (production host): Novagen / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P9WPA7, pantothenate kinase

-
Non-polymers , 5 types, 204 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 3.68 Å3/Da / Density % sol: 66.61 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 295 K / Method: microbatch / pH: 7.5
Details: 2% PEG 400, 2.0 M Ammonium sulphate, 100mM HEPES sodium salt

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.95372 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 31, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.26→43.55 Å / Num. obs: 49403 / % possible obs: 99.7 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 15.5
Reflection shellResolution: 2.26→2.38 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 7188 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GEU

2geu


Resolution: 2.26→43.55 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.504 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22796 2500 5.1 %RANDOM
Rwork0.19098 ---
obs0.19285 46901 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.687 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å2-0.35 Å2-0 Å2
2---0.7 Å2-0 Å2
3---2.28 Å2
Refinement stepCycle: 1 / Resolution: 2.26→43.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4652 0 123 178 4953
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194871
X-RAY DIFFRACTIONr_bond_other_d0.0060.024713
X-RAY DIFFRACTIONr_angle_refined_deg2.0451.9746595
X-RAY DIFFRACTIONr_angle_other_deg1.007310747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6345594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.44522.455220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.25215754
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1231549
X-RAY DIFFRACTIONr_chiral_restr0.1320.2748
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215413
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021140
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.9623.9242373
X-RAY DIFFRACTIONr_mcbond_other3.9573.9232372
X-RAY DIFFRACTIONr_mcangle_it5.8155.8682962
X-RAY DIFFRACTIONr_mcangle_other5.8155.8682963
X-RAY DIFFRACTIONr_scbond_it4.8584.4852498
X-RAY DIFFRACTIONr_scbond_other4.8564.4852482
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.3126.4863608
X-RAY DIFFRACTIONr_long_range_B_refined9.69332.0955592
X-RAY DIFFRACTIONr_long_range_B_other9.69232.0945592
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.259→2.318 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 211 -
Rwork0.273 3444 -
obs--100 %

+
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