[English] 日本語
Yorodumi
- PDB-2omk: Structure of the Bacteroides Thetaiotaomicron Thiamin Pyrophospho... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2omk
TitleStructure of the Bacteroides Thetaiotaomicron Thiamin Pyrophosphokinase
ComponentsHypothetical protein
KeywordsTRANSFERASE / Succinimide / Thiamin Pyrophosphokinase / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


thiamine diphosphokinase activity / thiamine metabolic process / thiamine diphosphate biosynthetic process / kinase activity / ATP binding
Similarity search - Function
Thiamin pyrophosphokinase / Thiamin pyrophosphokinase, catalytic domain / Thiamin pyrophosphokinase, catalytic domain superfamily / Thiamin pyrophosphokinase, catalytic domain / Thiamin pyrophosphokinase, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiamin pyrophosphokinase-like, catalytic domain
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsVorontsov, I.I. / Minasov, G. / Shuvalova, L. / Abdullah, J. / Collart, F.R. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of the Bacteroides Thetaiotaomicron Thiamin Pyrophosphokinase
Authors: Vorontsov, I.I. / Minasov, G. / Shuvalova, L. / Abdullah, J. / Collart, F.R. / Joachimiak, A. / Anderson, W.F.
History
DepositionJan 22, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id
Revision 3.0Feb 7, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_database_remark / pdbx_poly_seq_scheme / pdbx_validate_main_chain_plane / struct_conn / struct_ref / struct_ref_seq_dif
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.group_PDB / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref.pdbx_align_begin

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical protein
B: Hypothetical protein


Theoretical massNumber of molelcules
Total (without water)51,5522
Polymers51,5522
Non-polymers00
Water8,827490
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-15 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.309, 66.084, 57.552
Angle α, β, γ (deg.)90.00, 99.90, 90.00
Int Tables number4
Space group name H-MP1211
DetailsChains A and B represent a biological assembly which is a dimer

-
Components

#1: Protein Hypothetical protein /


Mass: 25775.906 Da / Num. of mol.: 2 / Mutation: V11I, D38(SNN), G39(ACY)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: BT_2397 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8A545, thiamine diphosphokinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 490 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: 0.05 M Potassium phosphate monobasic, 20 % w/v Polyethylene glycol 8000, pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 5ID-B11
SYNCHROTRONAPS 21-ID-D20.9787
Detector
TypeIDDetectorDateDetails
MARRESEARCH1CCDApr 17, 2006Mirrors
MARRESEARCH2CCDDec 17, 2006Mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 channelSINGLE WAVELENGTHMx-ray1
2Si 111 channelSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97871
ReflectionResolution: 1.8→45 Å / Num. all: 36873 / Num. obs: 36873 / % possible obs: 94.8 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 23.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 5.5 / Num. unique all: 2577 / % possible all: 67.1

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
SHELXphasing
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.658 / SU ML: 0.084 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20025 1829 5 %RANDOM
Rwork0.16454 ---
obs0.1664 34895 95.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.827 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å20.46 Å2
2---0.66 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3344 0 0 490 3834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223745
X-RAY DIFFRACTIONr_angle_refined_deg1.0941.9565110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9645481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.90824.719178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64115620
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5511518
X-RAY DIFFRACTIONr_chiral_restr0.0730.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022943
X-RAY DIFFRACTIONr_nbd_refined0.180.21803
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22558
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2437
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.251
X-RAY DIFFRACTIONr_mcbond_it0.8151.52371
X-RAY DIFFRACTIONr_mcangle_it1.34123750
X-RAY DIFFRACTIONr_scbond_it2.02731555
X-RAY DIFFRACTIONr_scangle_it3.0964.51360
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 96 -
Rwork0.213 1762 -
obs-1762 65.79 %

+
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