[English] 日本語
Yorodumi
- PDB-8tcc: GTP Cyclohydrolase-IB with dehydrocostus lactone -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8tcc
TitleGTP Cyclohydrolase-IB with dehydrocostus lactone
ComponentsGTP cyclohydrolase FolE2
KeywordsHYDROLASE/INHIBITOR / Cyclohydrolase / GTP / dehydrocostus lactone / fole2 / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


GTP cyclohydrolase I / GTP cyclohydrolase I activity / tetrahydrofolate biosynthetic process / metal ion binding
Similarity search - Function
GTP cyclohydrolase FolE2/MptA / GTP cyclohydrolase FolE2 / Type I GTP cyclohydrolase folE2
Similarity search - Domain/homology
: / SULFITE ION / : / GTP cyclohydrolase FolE2
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsMcWhorter, K.L. / Amaya Lopez, C.Y. / Davis, K.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM147557 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Combatting melioidosis with chemical synthetic lethality.
Authors: Zhang, Y. / McWhorter, K.L. / Rosen, P.C. / Klaus, J.R. / Gallant, E. / Amaya Lopez, C.Y. / Jhunjhunwala, R. / Chandler, J.R. / Davis, K.M. / Seyedsayamdost, M.R.
History
DepositionJun 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Nov 20, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GTP cyclohydrolase FolE2
B: GTP cyclohydrolase FolE2
C: GTP cyclohydrolase FolE2
D: GTP cyclohydrolase FolE2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,20111
Polymers135,2454
Non-polymers9567
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13820 Å2
ΔGint-77 kcal/mol
Surface area37410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.314, 71.319, 193.018
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
GTP cyclohydrolase FolE2


Mass: 33811.340 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: folE2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A069BB45, GTP cyclohydrolase I

-
Non-polymers , 5 types, 48 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO3 / SULFITE ION


Mass: 80.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO3
#5: Chemical ChemComp-ZS9 / dehydrocostus lactone, bound form


Mass: 232.318 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C15H20O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.77 Å3/Da / Density % sol: 30.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium chloride, 0.1 M Bis-Tris, 1.3-1.7 M ammonium sulfate, 0.01 M cadmium chloride
PH range: 6.3-6.8

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 13, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.1→48.25 Å / Num. obs: 17590 / % possible obs: 96.85 % / Redundancy: 9.8 % / Biso Wilson estimate: 62.65 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.2474 / Rpim(I) all: 0.07916 / Rrim(I) all: 0.2606 / Net I/σ(I): 10.13
Reflection shellResolution: 3.1→3.211 Å / Redundancy: 10 % / Rmerge(I) obs: 1.149 / Mean I/σ(I) obs: 1.89 / Num. unique obs: 1716 / CC1/2: 0.834 / CC star: 0.954 / Rpim(I) all: 0.3566 / Rrim(I) all: 1.206 / % possible all: 97.55

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000v721.3data reduction
HKL-2000v721.3data scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→47.16 Å / SU ML: 0.5291 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.569
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3119 875 5.01 %
Rwork0.2882 16607 -
obs0.2895 17482 96.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.62 Å2
Refinement stepCycle: LAST / Resolution: 3.1→47.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6730 0 13 41 6784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00946876
X-RAY DIFFRACTIONf_angle_d1.32959450
X-RAY DIFFRACTIONf_chiral_restr0.09111162
X-RAY DIFFRACTIONf_plane_restr0.00841241
X-RAY DIFFRACTIONf_dihedral_angle_d15.50312194
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.290.37241390.3312724X-RAY DIFFRACTION97.25
3.29-3.550.34411490.32142712X-RAY DIFFRACTION96.85
3.55-3.910.39351400.31252710X-RAY DIFFRACTION96.51
3.91-4.470.23991410.27322745X-RAY DIFFRACTION96.23
4.47-5.630.28331500.25312770X-RAY DIFFRACTION96.95
5.63-47.160.30981560.28592946X-RAY DIFFRACTION97.58

+
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