[English] 日本語
Yorodumi
- PDB-3epn: Crystal structure of Caulobacter crescentus ThiC complexed with i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3epn
TitleCrystal structure of Caulobacter crescentus ThiC complexed with imidazole ribonucleotide
ComponentsThiamine biosynthesis protein thiC
KeywordsBIOSYNTHETIC PROTEIN / Alpha-Beta Barrel / SAM superfamily / Thiamine biosynthesis
Function / homology
Function and homology information


4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase activity / phosphomethylpyrimidine synthase / carbon-carbon lyase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / 4 iron, 4 sulfur cluster binding / zinc ion binding
Similarity search - Function
ThiC-associated domain / ThiC-associated domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #620 / Radical SAM ThiC family, central domain / Phosphomethylpyrimidine synthase ThiC/5-hydroxybenzimidazole synthase BzaA/B / Phosphomethylpyrimidine synthase / ThiC/Bza, core domain / Radical SAM ThiC family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular ...ThiC-associated domain / ThiC-associated domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #620 / Radical SAM ThiC family, central domain / Phosphomethylpyrimidine synthase ThiC/5-hydroxybenzimidazole synthase BzaA/B / Phosphomethylpyrimidine synthase / ThiC/Bza, core domain / Radical SAM ThiC family / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-IRN / Phosphomethylpyrimidine synthase
Similarity search - Component
Biological speciesCaulobacter crescentus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.11 Å
AuthorsLi, S. / Chatterjee, A. / Zhang, Y. / Grove, T.L. / Lee, M. / Krebs, C. / Booker, S.J. / Begley, T.P. / Ealick, S.E.
CitationJournal: Nat.Chem.Biol. / Year: 2008
Title: Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily
Authors: Chatterjee, A. / Li, Y. / Zhang, Y. / Grove, T.L. / Lee, M. / Krebs, C. / Booker, S.J. / Begley, T.P. / Ealick, S.E.
History
DepositionSep 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software / Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Thiamine biosynthesis protein thiC
B: Thiamine biosynthesis protein thiC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,6734
Polymers136,1122
Non-polymers5602
Water9,242513
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-49 kcal/mol
Surface area34610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.603, 102.738, 82.635
Angle α, β, γ (deg.)90.000, 102.050, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Thiamine biosynthesis protein thiC


Mass: 68056.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter crescentus (bacteria) / Gene: thiC / Plasmid: pDESTF1 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9A6Q5
#2: Chemical ChemComp-IRN / 1-(5-O-phosphono-beta-D-ribofuranosyl)-1H-imidazole


Type: RNA linking / Mass: 280.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N2O7P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 513 / 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: 1.91 Å3/Da / Density % sol: 35.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4 M sodium citrate, 0.1 M sodium HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.11→50 Å / Num. all: 52752 / Num. obs: 52600 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.164 / Rsym value: 0.164 / Χ2: 2.047
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.11-2.191.60.31743851.01875.1
2.19-2.271.80.28447331.07381.1
2.27-2.3820.27749371.09784.9
2.38-2.52.20.28351861.25988.3
2.5-2.662.50.26953151.20491.4
2.66-2.862.80.26655321.94694.5
2.86-3.153.20.24257482.36998.3
3.15-3.613.50.18557262.14297.9
3.61-4.543.40.11955842.62594.8
4.54-503.40.08556062.84894

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementResolution: 2.11→35.24 Å / Occupancy max: 1 / Occupancy min: 0.27 / FOM work R set: 0.81 / SU ML: 0.33 / σ(F): 1.37 / Phase error: 26.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2653 5.04 %random
Rwork0.168 ---
obs0.172 52600 89.06 %-
all-52752 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.823 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso max: 162.06 Å2 / Biso mean: 25.361 Å2 / Biso min: 2.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.988 Å20 Å2-0.357 Å2
2---0.643 Å20 Å2
3----0.344 Å2
Refinement stepCycle: LAST / Resolution: 2.11→35.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8166 0 36 513 8715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068400
X-RAY DIFFRACTIONf_angle_d0.99611413
X-RAY DIFFRACTIONf_chiral_restr0.0681237
X-RAY DIFFRACTIONf_plane_restr0.0051502
X-RAY DIFFRACTIONf_dihedral_angle_d17.4763105
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.11-2.1450.275920.1811755184760
2.145-2.1870.3241120.1742245235776
2.187-2.2310.291300.172374250480
2.231-2.280.2571380.1722355249382
2.28-2.3330.31320.1842482261485
2.333-2.3910.2811290.22520264985
2.391-2.4560.3241510.1982571272288
2.456-2.5280.2961500.1912630278089
2.528-2.6090.261140.1912714282891
2.609-2.7030.2931540.1772678283292
2.703-2.8110.2711510.1782777292894
2.811-2.9390.2941640.1742880304497
2.939-3.0940.2421380.1722892303098
3.094-3.2870.2491330.162944307799
3.287-3.5410.2421530.1552881303498
3.541-3.8970.211530.1422822297596
3.897-4.460.1891440.1282817296195
4.46-5.6150.1691590.1432782294194
5.615-35.2450.2471560.1912828298493

+
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