[English] 日本語
Yorodumi
- PDB-3af0: Pantothenate kinase from Mycobacterium tuberculosis (MtPanK) in c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3af0
TitlePantothenate kinase from Mycobacterium tuberculosis (MtPanK) in complex with GDP and Pantothenate
ComponentsPantothenate kinase
KeywordsTRANSFERASE / Homodimer / COA biosynthesis / Nucleotide binding / ATP-binding / Kinase / Nucleotide-binding
Function / homology
Function and homology information


pantothenate kinase / pantothenate kinase activity / coenzyme A biosynthetic process / 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
GUANOSINE-5'-DIPHOSPHATE / PANTOTHENOIC ACID / Pantothenate kinase / Pantothenate kinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChetnani, B. / Kumar, P. / Surolia, A. / Vijayan, M.
CitationJournal: 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.
History
DepositionFeb 19, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 29, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,23213
Polymers35,7051
Non-polymers1,52712
Water3,153175
1
A: Pantothenate kinase
hetero molecules

A: Pantothenate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,46326
Polymers71,4102
Non-polymers3,05324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3910 Å2
ΔGint-31 kcal/mol
Surface area27610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.730, 104.730, 90.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Pantothenate kinase / MtPanK / Pantothenic acid kinase


Mass: 35704.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: coaA, Rv1092c / Plasmid: PET-28a(+) (NOVAGEN) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P63810, UniProt: P9WPA7*PLUS, pantothenate kinase

-
Non-polymers , 5 types, 187 molecules

#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-PAU / PANTOTHENOIC ACID / N-[(2R)-2,4-DIHYDROXY-3,3-DIMETHYLBUTANOYL]-BETA-ALANINE


Type: peptide-like / Mass: 219.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H17NO5
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 4.01 Å3/Da / Density % sol: 69.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.4-1.8M trisodium citrate, 0.05-0.1M sodium acetate, 10% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 19, 2009 / Details: Mirrors
RadiationMonochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 20208 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 65.7 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 13
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 2 / Num. unique all: 2893 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GEV

2gev


Resolution: 2.5→34.28 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.304 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.2539 981 4.9 %RANDOM
Rwork0.20651 ---
obs0.2088 19194 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.796 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20.65 Å20 Å2
2--1.3 Å20 Å2
3----1.94 Å2
Refinement stepCycle: LAST / Resolution: 2.5→34.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2474 0 98 175 2747
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0222623
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.9923561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6595306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.22422.222126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.31415414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4051530
X-RAY DIFFRACTIONr_chiral_restr0.0990.2394
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211984
X-RAY DIFFRACTIONr_mcbond_it1.5381.51546
X-RAY DIFFRACTIONr_mcangle_it2.86822503
X-RAY DIFFRACTIONr_scbond_it4.31431077
X-RAY DIFFRACTIONr_scangle_it6.8684.51058
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 70 -
Rwork0.361 1401 -
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://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