[English] 日本語
Yorodumi
- PDB-4pzv: Crystal structure of Francisella tularensis HPPK-DHPS in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pzv
TitleCrystal structure of Francisella tularensis HPPK-DHPS in complex with bisubstrate analog HPPK inhibitor J1D
Components2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase/dihydropteroate synthase
KeywordsTRANSFERASE / Ferredoxin-like fold / TIM barrel fold / ATP binding / Phosphorylation
Function / homology
Function and homology information


2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / kinase activity / ATP binding
Similarity search - Function
7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase, HPPK / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK superfamily / 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK) / Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. ...7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase, HPPK / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK superfamily / 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK) / Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / Alpha-Beta Plaits / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-J1D / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.704 Å
AuthorsShaw, G.X. / Shi, G. / Ji, X.
Citation
Journal: Febs J. / Year: 2014
Title: Structural enzymology and inhibition of the bi-functional folate pathway enzyme HPPK-DHPS from the biowarfare agent Francisella tularensis.
Authors: Shaw, G.X. / Li, Y. / Shi, G. / Wu, Y. / Cherry, S. / Needle, D. / Zhang, D. / Tropea, J.E. / Waugh, D.S. / Yan, H. / Ji, X.
#1: Journal: J.Med.Chem. / Year: 2001
Title: Bisubstrate analogue inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: synthesis and biochemical and crystallographic studies.
Authors: Shi, G. / Blaszczyk, J. / Ji, X. / Yan, H.
#2: Journal: Bioorg.Med.Chem. / Year: 2012
Title: Bisubstrate analogue inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: New design with improved properties.
Authors: Shi, G. / Shaw, G. / Liang, Y.H. / Subburaman, P. / Li, Y. / Wu, Y. / Yan, H. / Ji, X.
#3: Journal: Bioorg.Med.Chem. / Year: 2012
Title: Bisubstrate analog inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase: new lead exhibits a distinct binding mode.
Authors: Shi, G. / Shaw, G. / Li, Y. / Wu, Y. / Yan, H. / Ji, X.
History
DepositionMar 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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
Revision 1.3Sep 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase/dihydropteroate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3839
Polymers48,3141
Non-polymers1,0698
Water7,746430
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.945, 74.434, 69.758
Angle α, β, γ (deg.)90.000, 93.200, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase/dihydropteroate synthase


Mass: 48313.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: SCHU S4 / Schu 4 / Gene: foIK, folK, FTT_0942c / Plasmid: pDN2163 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: Q5NGA7, dihydropteroate synthase, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase
#2: Chemical ChemComp-J1D / 5'-{[2-({N-[(2-amino-7,7-dimethyl-4-oxo-3,4,7,8-tetrahydropteridin-6-yl)carbonyl]glycyl}amino)ethyl]sulfonyl}-5'-deoxyadenosine


Mass: 634.625 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H30N12O8S
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 430 / 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: 2.3 Å3/Da / Density % sol: 46.62 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG monomethyl ether 2000, NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 18, 2012 / Details: mirrors
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 43013 / Num. obs: 43013 / % possible obs: 90 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.087 / Χ2: 1.001 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.7-1.761.90.4051.934160.99972.1
1.76-1.832.20.3812.138530.95580.9
1.83-1.912.50.3812.340201.00584.9
1.91-2.022.90.3552.742211.00388.9
2.02-2.143.30.3123.544571.00692.8
2.14-2.313.50.2434.544410.99993.5
2.31-2.543.70.19645181.00394.5
2.54-2.9140.133945721.00495.5
2.91-3.664.80.06519.746971.00498
3.66-305.20.03441.448181.00599

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
Blu-Ice5data collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3UDE and 1TWS
Resolution: 1.704→28.106 Å / SU ML: 0.29 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 27.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.259 979 2.28 %Random
Rwork0.2104 ---
all0.2145 43002 --
obs0.2115 43002 89.74 %-
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 52.3 Å2 / Biso mean: 18.4151 Å2 / Biso min: 4.09 Å2
Refinement stepCycle: LAST / Resolution: 1.704→28.106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3339 0 72 430 3841
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093665
X-RAY DIFFRACTIONf_angle_d1.0754957
X-RAY DIFFRACTIONf_chiral_restr0.062560
X-RAY DIFFRACTIONf_plane_restr0.005636
X-RAY DIFFRACTIONf_dihedral_angle_d12.5191444
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.704-1.79380.38431030.359747924895489572
1.7938-1.90620.37171300.328455815711571184
1.9062-2.05330.31211270.266759726099609989
2.0533-2.25990.27481430.22362176360636093
2.2599-2.58670.27891600.191362816441644194
2.5867-3.25820.22821500.180864606610661096
3.2582-28.11010.20921660.164467206886688699

+
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