[English] 日本語
Yorodumi
- PDB-4h65: Crystal structure of SeMet derivative of HMP synthase Thi5 from S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4h65
TitleCrystal structure of SeMet derivative of HMP synthase Thi5 from S. cerevisiae
ComponentsPyrimidine precursor biosynthesis enzyme THI5
KeywordsTRANSFERASE / HMP-P synthase / THI5-PLP complex / PLP binding
Function / homology
Function and homology information


4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase activity from histidine and PLP / Transferases / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / iron ion binding
Similarity search - Function
NMT1/THI5 family / SsuA/THI5-like / NMT1/THI5 like / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate synthase THI5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsCoquille, S.C. / Roux, C. / Fitzpatrick, T. / Thore, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: The Last Piece in the Vitamin B1 Biosynthesis Puzzle: STRUCTURAL AND FUNCTIONAL INSIGHT INTO YEAST 4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE PHOSPHATE (HMP-P) SYNTHASE.
Authors: Coquille, S. / Roux, C. / Fitzpatrick, T.B. / Thore, S.
History
DepositionSep 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Jan 23, 2013Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pyrimidine precursor biosynthesis enzyme THI5
B: Pyrimidine precursor biosynthesis enzyme THI5


Theoretical massNumber of molelcules
Total (without water)79,5032
Polymers79,5032
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-2 kcal/mol
Surface area26440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.440, 109.210, 122.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Pyrimidine precursor biosynthesis enzyme THI5 / HMP synthase Thi5


Mass: 39751.418 Da / Num. of mol.: 2 / Mutation: K240S, E241G, Q317T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: THI5, YFL058W / Production host: Escherichia coli (E. coli) / References: UniProt: P43534
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 0.2 M potassium thiocyanate, 0.1 M Bis-Tris, pH 5.7, 27% PEG3350, 10% dodecyl-beta-D-maltoside, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97795 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jan 26, 2012
RadiationMonochromator: Bartels Monochromator with dual channel cut crystals (DCCM)
Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97795 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 24546 / Num. obs: 24539 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 19.37 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 25.14
Reflection shellResolution: 2.55→2.62 Å / Redundancy: 19.39 % / Rmerge(I) obs: 1.293 / Mean I/σ(I) obs: 2.85 / Num. unique all: 3224 / % possible all: 100

-
Processing

Software
NameVersionClassification
XDSdata scaling
CCP4model building
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→19.998 Å / SU ML: 0.41 / σ(F): 1.44 / Phase error: 27.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2542 2011 8.2 %RANDOM
Rwork0.2106 ---
obs0.2141 24535 99.98 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 12.056 Å2 / ksol: 0.263 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-17.7609 Å20 Å20 Å2
2--38.9729 Å20 Å2
3---9.7506 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4608 0 0 109 4717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014714
X-RAY DIFFRACTIONf_angle_d1.3126371
X-RAY DIFFRACTIONf_dihedral_angle_d15.1191756
X-RAY DIFFRACTIONf_chiral_restr0.086693
X-RAY DIFFRACTIONf_plane_restr0.007806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.63560.38441340.31521539X-RAY DIFFRACTION100
2.6356-2.67310.37061430.29881591X-RAY DIFFRACTION100
2.6731-2.71290.37551430.29951616X-RAY DIFFRACTION100
2.7129-2.75520.31181410.29981558X-RAY DIFFRACTION100
2.7552-2.80030.3181380.27951565X-RAY DIFFRACTION100
2.8003-2.84840.33141480.28921606X-RAY DIFFRACTION100
2.8484-2.90010.32331420.26871579X-RAY DIFFRACTION100
2.9001-2.95570.33131400.26141567X-RAY DIFFRACTION100
2.9557-3.01580.33421440.27091601X-RAY DIFFRACTION100
3.0158-3.08120.28991420.25881599X-RAY DIFFRACTION100
3.0812-3.15260.34441420.26041558X-RAY DIFFRACTION100
3.1526-3.23110.31171370.25121597X-RAY DIFFRACTION100
3.2311-3.31810.26581420.23311581X-RAY DIFFRACTION100
3.3181-3.41520.25261460.21141617X-RAY DIFFRACTION100
3.4152-3.52490.26571400.21711570X-RAY DIFFRACTION100
3.5249-3.65020.25151420.2161586X-RAY DIFFRACTION100
3.6502-3.79540.31251400.19361565X-RAY DIFFRACTION100
3.7954-3.96680.19881450.1891580X-RAY DIFFRACTION100
3.9668-4.17420.17741410.16891605X-RAY DIFFRACTION100
4.1742-4.4330.2161350.16021586X-RAY DIFFRACTION100
4.433-4.7710.17751420.16471571X-RAY DIFFRACTION100
4.771-5.24330.23371390.16561593X-RAY DIFFRACTION100
5.2433-5.98410.29011380.21891596X-RAY DIFFRACTION100
5.9841-7.47340.26681460.21361577X-RAY DIFFRACTION100
7.4734-19.99820.22231460.20411580X-RAY DIFFRACTION100

+
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