[English] 日本語
Yorodumi
- PDB-2i5b: The crystal structure of an ADP complex of Bacillus subtilis pyri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2i5b
TitleThe crystal structure of an ADP complex of Bacillus subtilis pyridoxal kinase provides evidence for the parralel emergence of enzyme activity during evolution
ComponentsPhosphomethylpyrimidine kinase
KeywordsTRANSFERASE / ADP complex / PdxK / thiD / ribokinase superfamily
Function / homology
Function and homology information


phosphomethylpyrimidine kinase activity / hydroxymethylpyrimidine kinase activity / pyridoxal kinase activity / pyridoxal kinase / thiamine biosynthetic process / ATP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
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 / Pyridoxine kinase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsNewman, J.A. / Das, S.K. / Sedelnikova, S.E. / Rice, D.W.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: The Crystal Structure of an ADP Complex of Bacillus subtilis Pyridoxal Kinase Provides Evidence for the Parallel Emergence of Enzyme Activity During Evolution.
Authors: Newman, J.A. / Das, S.K. / Sedelnikova, S.E. / Rice, D.W.
#1: Journal: To be published
Title: Cloning, purification and preliminary crystallographic analysis of a putative Pyridoxal Kinase from Bacillus subtilis
History
DepositionAug 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 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: Phosphomethylpyrimidine kinase
C: Phosphomethylpyrimidine kinase
D: Phosphomethylpyrimidine kinase
B: Phosphomethylpyrimidine kinase
E: Phosphomethylpyrimidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,37210
Polymers145,2365
Non-polymers2,1365
Water00
1
A: Phosphomethylpyrimidine kinase
B: Phosphomethylpyrimidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9494
Polymers58,0942
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-34 kcal/mol
Surface area19480 Å2
MethodPISA
2
C: Phosphomethylpyrimidine kinase
D: Phosphomethylpyrimidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9494
Polymers58,0942
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-35 kcal/mol
Surface area19440 Å2
MethodPISA
3
E: Phosphomethylpyrimidine kinase
hetero molecules

E: Phosphomethylpyrimidine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9494
Polymers58,0942
Non-polymers8542
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Unit cell
Length a, b, c (Å)102.499, 102.499, 251.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
12B
13C
14D
/ NCS ensembles :
IDDetails
1A
2B
3C
4D
DetailsThe biological assembly is a dimer formed between chanis A and B and by chains C and D

-
Components

#1: Protein
Phosphomethylpyrimidine kinase / HMP-phosphate kinase / HMP-P kinase


Mass: 29047.225 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: thiD / Plasmid: pTB361 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P39610, phosphooxymethylpyrimidine kinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.86 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 28% peg 4000, 0.17M sodium acetate trihydrate, 0.1M Tris HCL (pH 8.5), 10mM MgCl, 10mM ADP, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 9, 2005
RadiationMonochromator: Osmic Varimax mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.8→94.916 Å / Num. all: 33604 / Num. obs: 33604 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 50.3 Å2 / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 5.7
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 1.7 / Num. measured all: 18268 / Num. unique all: 4844 / Rsym value: 0.475 / % possible all: 99.9

-
Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
MAR345345DTBdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UB0

1ub0


Resolution: 2.8→12.87 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.865 / SU B: 15.994 / SU ML: 0.317 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.441 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1688 5.1 %RANDOM
Rwork0.222 ---
all0.225 33305 --
obs0.225 33305 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.436 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.8→12.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9932 0 135 0 10067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02210231
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.98613911
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.29551320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.8526.492382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.133151773
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.0381515
X-RAY DIFFRACTIONr_chiral_restr0.0940.21669
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027408
X-RAY DIFFRACTIONr_nbd_refined0.2190.24919
X-RAY DIFFRACTIONr_nbtor_refined0.3110.26999
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2331
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3580.2108
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.430.28
X-RAY DIFFRACTIONr_mcbond_it0.5761.56721
X-RAY DIFFRACTIONr_mcangle_it0.991210592
X-RAY DIFFRACTIONr_scbond_it1.14533895
X-RAY DIFFRACTIONr_scangle_it1.9364.53319
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1978TIGHT POSITIONAL0.060.05
1A1978TIGHT THERMAL0.330.5
2B1978TIGHT POSITIONAL0.050.05
2B1978TIGHT THERMAL0.320.5
3C1903TIGHT POSITIONAL0.060.05
3C1903TIGHT THERMAL0.140.5
4D1978TIGHT POSITIONAL0.050.05
4D1978TIGHT THERMAL0.330.5
LS refinement shellResolution: 2.8→2.869 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 126 -
Rwork0.276 2205 -
obs-2331 99.74 %

+
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