[English] 日本語
Yorodumi
- PDB-4c5k: Structure of the pyridoxal kinase from Staphylococcus aureus in c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4c5k
TitleStructure of the pyridoxal kinase from Staphylococcus aureus in complex with ADP
ComponentsPHOSPHOMETHYLPYRIMIDINE KINASE
KeywordsTRANSFERASE / RIBOKINASE
Function / homology
Function and homology information


phosphomethylpyrimidine kinase activity / hydroxymethylpyrimidine kinase activity / pyridoxal kinase / thiamine biosynthetic process / nucleotide binding / cytosol
Similarity search - Function
Hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase / Hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase domain / 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 kinase / Phosphomethylpyrimidine kinase
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS SUBSP. AUREUS MU50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsNodwell, M. / Alte, F. / Sieber, S.A. / Schneider, S.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: A Subfamily of Bacterial Ribokinases Utilizes a Hemithioacetal for Pyridoxal Phosphate Salvage.
Authors: Nodwell, M.B. / Koch, M.F. / Alte, F. / Schneider, S. / Sieber, S.A.
History
DepositionSep 12, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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: PHOSPHOMETHYLPYRIMIDINE KINASE
B: PHOSPHOMETHYLPYRIMIDINE KINASE
C: PHOSPHOMETHYLPYRIMIDINE KINASE
D: PHOSPHOMETHYLPYRIMIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,20521
Polymers119,2474
Non-polymers2,95817
Water16,646924
1
B: PHOSPHOMETHYLPYRIMIDINE KINASE
D: PHOSPHOMETHYLPYRIMIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,15011
Polymers59,6242
Non-polymers1,5279
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-121.8 kcal/mol
Surface area19820 Å2
MethodPISA
2
A: PHOSPHOMETHYLPYRIMIDINE KINASE
C: PHOSPHOMETHYLPYRIMIDINE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,05410
Polymers59,6242
Non-polymers1,4318
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-113.3 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.460, 100.360, 167.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9991, -0.0069, 0.0417), (0.0053, 0.9993, 0.0376), (-0.0419, -0.0373, 0.9984)-0.3017, 0.2231, 43.1731
2given(-0.9845, 0.0097, 0.1754), (-0.0113, -0.9999, -0.008), (0.1753, -0.0099, 0.9845)37.6815, -5.8369, -3.4252
3given(-0.9916, -0.0162, 0.1285), (0.0051, -0.9963, -0.0863), (0.1294, -0.0849, 0.9879)44.9982, -9.9277, 39.1265

-
Components

#1: Protein
PHOSPHOMETHYLPYRIMIDINE KINASE / PYRIDOXAL KINASE


Mass: 29811.793 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS SUBSP. AUREUS MU50 (bacteria)
Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q99W31, UniProt: A0A0H3JTP0*PLUS, pyridoxal 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 924 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFIRST AMINO ACID IS A GLY INSTEAD OF MET DUE TO REMOVAL OF THE AFFINITY TAG

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growDetails: 50MM HEPES, 2M NAH4SO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Jul 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→48.78 Å / Num. obs: 200707 / % possible obs: 97.1 % / Observed criterion σ(I): 1 / Redundancy: 8.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 23.35
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 2 / % possible all: 93.1

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C5J

4c5j


Resolution: 1.4→48.78 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.884 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16519 10053 5 %RANDOM
Rwork0.12794 ---
obs0.12983 190654 97.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.569 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.4→48.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8259 0 173 924 9356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.028749
X-RAY DIFFRACTIONr_bond_other_d0.0010.028269
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.98611934
X-RAY DIFFRACTIONr_angle_other_deg0.901319123
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.38751138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72826.14342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.984151477
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.5971510
X-RAY DIFFRACTIONr_chiral_restr0.1050.21385
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029841
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021817
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_it2.991.8824427
X-RAY DIFFRACTIONr_mcbond_other2.991.8824426
X-RAY DIFFRACTIONr_mcangle_it3.3592.8355537
X-RAY DIFFRACTIONr_mcangle_other3.3592.8355538
X-RAY DIFFRACTIONr_scbond_it4.0142.2434322
X-RAY DIFFRACTIONr_scbond_other3.8842.2164267
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5243.1996290
X-RAY DIFFRACTIONr_long_range_B_refined4.72416.83410618
X-RAY DIFFRACTIONr_long_range_B_other4.37816.14810156
X-RAY DIFFRACTIONr_rigid_bond_restr4.251317018
X-RAY DIFFRACTIONr_sphericity_free31.2085233
X-RAY DIFFRACTIONr_sphericity_bonded13.802517540
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 719 -
Rwork0.249 13343 -
obs--92.9 %

+
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