[English] 日本語
Yorodumi
- PDB-1rfu: Crystal structure of pyridoxal kinase complexed with ADP and PLP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rfu
TitleCrystal structure of pyridoxal kinase complexed with ADP and PLP
Componentspyridoxal kinase
KeywordsTRANSFERASE
Function / homology
Function and homology information


pyridoxal kinase activity / pyridoxal 5'-phosphate salvage / pyridoxal kinase / ATP binding / metal ion binding / cytosol
Similarity search - Function
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
ADENOSINE-5'-DIPHOSPHATE / PYRIDOXAL-5'-PHOSPHATE / Pyridoxal kinase
Similarity search - Component
Biological speciesOvis aries (sheep)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLiang, D.-C. / Jiang, T. / Li, M.-H.
Citation
Journal: J.BIOL.CHEM. / Year: 2004
Title: Conformational changes in the reaction of pyridoxal kinase
Authors: Li, M.-H. / Kwok, F. / Chang, W.-R. / Liu, S.-Q. / Lo, S.C.L. / Zhang, J.-P. / Jiang, T. / Liang, D.-C.
#1: Journal: J.Biol.Chem. / Year: 2002
Title: Crystal Structure of Brain Pyridoxal Kinase, a Novel Member of the Ribokinase Superfamily
Authors: Li, M.-H. / Kwok, F. / Chang, W.-R. / Lau, C.-K. / Zhang, J.-P. / Lo, S.C.L. / Jiang, T. / Liang, D.-C.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Crystallization and preliminary crystallographic studies of pyridoxal kinase from sheep brain
Authors: Li, M.-H. / Kwok, F. / An, X.-M. / Chang, W.-R. / Lau, C.-K. / Zhang, J.-P. / Liu, S.-Q. / Leung, Y.-C. / Jiang, T. / Liang, D.-C.
History
DepositionNov 10, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: pyridoxal kinase
B: pyridoxal kinase
C: pyridoxal kinase
D: pyridoxal kinase
E: pyridoxal kinase
F: pyridoxal kinase
G: pyridoxal kinase
H: pyridoxal kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,80532
Polymers278,8878
Non-polymers5,91824
Water4,810267
1
A: pyridoxal kinase
E: pyridoxal kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2018
Polymers69,7222
Non-polymers1,4806
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6990 Å2
ΔGint-103 kcal/mol
Surface area23490 Å2
MethodPISA
2
B: pyridoxal kinase
F: pyridoxal kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2018
Polymers69,7222
Non-polymers1,4806
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: pyridoxal kinase
H: pyridoxal kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2018
Polymers69,7222
Non-polymers1,4806
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-105 kcal/mol
Surface area23350 Å2
MethodPISA
4
D: pyridoxal kinase
G: pyridoxal kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2018
Polymers69,7222
Non-polymers1,4806
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.088, 109.088, 284.272
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
DetailsThe biological assembly is a homodimer. The eight monomers in the asymmetric unit form four such homodimers.

-
Components

#1: Protein
pyridoxal kinase / Pyridoxine kinase


Mass: 34860.879 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: P82197, pyridoxal kinase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 3.04 Å3/Da / Density % sol: 59.25 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: ammonium sulphate, potassium phosphate, ADP, PLP, zinc acetate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 12, 2002
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 86300 / Num. obs: 75513 / % possible obs: 87.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.4
Reflection shellResolution: 2.8→2.86 Å / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2.3 / Num. unique all: 5131 / % possible all: 95.2

-
Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LHP

1lhp


Resolution: 2.8→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
Details: used least squares procedure for hemihedral twinning, with a twinning operation of "h,-k,-l", and a twinning fraction of 0.5
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1971 -RANDOM
Rwork0.229 ---
all0.23 86300 --
obs0.23 75513 87.5 %-
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19512 0 344 267 20123
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5

+
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