[English] 日本語
Yorodumi
- PDB-5zw9: Crystal structure of Pyridoxal kinase (PdxK) from Salmonella typh... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zw9
TitleCrystal structure of Pyridoxal kinase (PdxK) from Salmonella typhimurium
ComponentsPyridoxalkinase
KeywordsTRANSFERASE / Pyridoxal kinase / bound phosphate / Salmonella typhimurium
Function / homology
Function and homology information


hydroxymethylpyrimidine kinase activity / pyridoxal kinase activity / pyridoxal 5'-phosphate salvage / pyridoxal kinase / phosphorylation / magnesium ion binding / zinc ion binding / ATP binding / cytosol
Similarity search - Function
Pyridoxine/pyridoxal/pyridoxamine kinase / Pyridoxine kinase / Pyridoxamine kinase/Phosphomethylpyrimidine kinase / Phosphomethylpyrimidine kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Pyridoxine/pyridoxal/pyridoxamine kinase / Pyridoxine/pyridoxal/pyridoxamine kinase
Similarity search - Component
Biological speciesSalmonella choleraesuis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDeka, G. / Benazir, J.F. / Kalyani, J.N. / Savithri, H.S. / Murthy, M.R.N.
Funding support India, 2items
OrganizationGrant numberCountry
Department of BiotechnologyBT/ PR7021/BRB/10/1142/2012 India
Department of Science and TechnologySR/S2/ JCB-12/2005/9.5.2006 India
CitationJournal: Febs J. / Year: 2019
Title: Structural and functional studies on Salmonella typhimurium pyridoxal kinase: the first structural evidence for the formation of Schiff base with the substrate.
Authors: Deka, G. / Kalyani, J.N. / Jahangir, F.B. / Sabharwal, P. / Savithri, H.S. / Murthy, M.R.N.
History
DepositionMay 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pyridoxalkinase
B: Pyridoxalkinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8939
Polymers64,1272
Non-polymers7667
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-35 kcal/mol
Surface area21890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.110, 72.890, 107.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 1 / Auth seq-ID: 16 - 283 / Label seq-ID: 16 - 283

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Pyridoxalkinase / PL kinase


Mass: 32063.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella choleraesuis (bacteria) / Strain: LT2 / Gene: pdxK / Plasmid: pET-22b(+) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: A0A0M0PWM4, UniProt: A0A0F7J8S0*PLUS, pyridoxal kinase

-
Non-polymers , 6 types, 170 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 1.92 Å3/Da / Density % sol: 36.04 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.5 / Details: 20% PEG 4000, 10% 2-propanol, 100 mM HEPES pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→72.89 Å / Num. obs: 14688 / % possible obs: 90.1 % / Redundancy: 5.6 % / Biso Wilson estimate: 21.7 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.06 / Rrim(I) all: 0.15 / Net I/σ(I): 9.9
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.48 / Num. unique obs: 2274 / CC1/2: 0.84 / Rpim(I) all: 0.22 / Rrim(I) all: 0.53 / % possible all: 98.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DDM

2ddm


Resolution: 2.6→60.33 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.844 / SU B: 16.747 / SU ML: 0.341 / Cross valid method: THROUGHOUT / ESU R Free: 0.433 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28923 730 5 %RANDOM
Rwork0.22375 ---
obs0.22697 13922 89.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.761 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2--3.53 Å2-0 Å2
3----3.27 Å2
Refinement stepCycle: 1 / Resolution: 2.6→60.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3881 0 49 163 4093
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194067
X-RAY DIFFRACTIONr_bond_other_d0.0030.023899
X-RAY DIFFRACTIONr_angle_refined_deg1.0381.9665552
X-RAY DIFFRACTIONr_angle_other_deg1.01738946
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.015534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.57424.459148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.70815618
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1871516
X-RAY DIFFRACTIONr_chiral_restr0.0510.2667
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214576
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02866
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_it0.8673.3382110
X-RAY DIFFRACTIONr_mcbond_other0.8673.3372109
X-RAY DIFFRACTIONr_mcangle_it1.5524.9962631
X-RAY DIFFRACTIONr_mcangle_other1.5524.9962632
X-RAY DIFFRACTIONr_scbond_it0.6973.4271957
X-RAY DIFFRACTIONr_scbond_other0.6963.4271957
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2395.0952915
X-RAY DIFFRACTIONr_long_range_B_refined3.80126.694653
X-RAY DIFFRACTIONr_long_range_B_other3.826.6954654
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCSNumber: 2221 / Type: tight thermal / Rms dev position: 2.55 Å / Weight position: 0.5
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 63 -
Rwork0.29 1075 -
obs--97.68 %

+
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://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