[English] 日本語
Yorodumi
- PDB-7mpy: Crystal structure of cytosolic HPPK-DHPS from A.thaliana -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mpy
TitleCrystal structure of cytosolic HPPK-DHPS from A.thaliana
ComponentsFolate synthesis bifunctional protein
KeywordsTRANSFERASE / Folate biosynthesis / herbicide target / PLANT PROTEIN
Function / homology
Function and homology information


2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase / dihydropteroate synthase / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / kinase activity / response to oxidative stress / ATP binding / metal ion binding / cytosol
Similarity search - Function
7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase signature. / Dihydropteroate synthase signature 1. / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase, HPPK / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK superfamily / 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK) / Dihydropteroate synthase / Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Dihydropteroate synthase-like / Pterin-binding domain ...7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase signature. / Dihydropteroate synthase signature 1. / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase, HPPK / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK superfamily / 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK) / Dihydropteroate synthase / Dihydropteroate synthase domain / Dihydropteroate synthase signature 2. / Dihydropteroate synthase-like / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Folate synthesis bifunctional protein
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsVadlamani, G. / Bond, C.S.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP190101048 Australia
CitationJournal: Plant Commun. / Year: 2022
Title: Crystal structure of Arabidopsis thaliana HPPK/DHPS, a bifunctional enzyme and target of the herbicide asulam.
Authors: Vadlamani, G. / Sukhoverkov, K.V. / Haywood, J. / Breese, K.J. / Fisher, M.F. / Stubbs, K.A. / Bond, C.S. / Mylne, J.S.
History
DepositionMay 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 20, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Folate synthesis bifunctional protein
B: Folate synthesis bifunctional protein


Theoretical massNumber of molelcules
Total (without water)112,5072
Polymers112,5072
Non-polymers00
Water2,972165
1
A: Folate synthesis bifunctional protein


Theoretical massNumber of molelcules
Total (without water)56,2531
Polymers56,2531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Folate synthesis bifunctional protein


Theoretical massNumber of molelcules
Total (without water)56,2531
Polymers56,2531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.680, 240.150, 148.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Folate synthesis bifunctional protein


Mass: 56253.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CytHPPK/DHPS, At1g69190, F23O10.22, F4N2.15 / Production host: Escherichia coli (E. coli)
References: UniProt: Q1ENB6, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase, dihydropteroate synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Crystals of 13-20 mg/ml HPPK-DHPS (purified in 20 mM HEPES pH 8.0, 125 mM sodium chloride, 2 mM dithiothreitol of buffer) were obtained in 30-40% PEG 3350 and 0.2M NaF

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 1, 2019
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→93.46 Å / Num. obs: 51863 / % possible obs: 96.9 % / Redundancy: 5.9 % / Biso Wilson estimate: 51.66 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.04 / Rrim(I) all: 0.1 / Net I/σ(I): 9.6
Reflection shellResolution: 2.3→2.37 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.639 / Num. unique obs: 3518 / CC1/2: 0.23 / Rpim(I) all: 0.377 / Rrim(I) all: 0.746 / % possible all: 77.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BMB

2bmb


Resolution: 2.3→93.46 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.865 / SU B: 29.942 / SU ML: 0.313 / Cross valid method: FREE R-VALUE / ESU R: 0.28 / ESU R Free: 0.268
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2998 3249 6.268 %
Rwork0.238 48587 -
all0.242 --
obs-51836 96.734 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 67.247 Å2
Baniso -1Baniso -2Baniso -3
1-6.057 Å20 Å20 Å2
2---5.568 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.3→93.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6679 0 0 165 6844
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136797
X-RAY DIFFRACTIONr_bond_other_d0.0020.0156739
X-RAY DIFFRACTIONr_angle_refined_deg1.61.6339162
X-RAY DIFFRACTIONr_angle_other_deg1.2231.58415521
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3555844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.98921.416353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.782151273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6881558
X-RAY DIFFRACTIONr_chiral_restr0.0650.2904
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027499
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021457
X-RAY DIFFRACTIONr_nbd_refined0.2050.21388
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.26416
X-RAY DIFFRACTIONr_nbtor_refined0.160.23227
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.23306
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2144
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.160.216
X-RAY DIFFRACTIONr_nbd_other0.2310.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1320.26
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.5091770.5022754X-RAY DIFFRACTION75.5218
2.424-2.4950.4712220.4543310X-RAY DIFFRACTION94.7679
2.571-2.6560.3872360.3773263X-RAY DIFFRACTION100
2.656-2.7490.3532170.3483146X-RAY DIFFRACTION100
2.749-2.8530.332040.3263101X-RAY DIFFRACTION100
2.853-2.9690.3171960.2762949X-RAY DIFFRACTION100
2.969-3.1010.3131860.2412824X-RAY DIFFRACTION100
3.101-3.2520.2881830.2352737X-RAY DIFFRACTION100
3.252-3.4280.2951700.22598X-RAY DIFFRACTION100
3.428-3.6360.3061630.1982455X-RAY DIFFRACTION99.9237
3.636-3.8860.2831550.1872317X-RAY DIFFRACTION99.5971
3.886-4.1970.2551420.1662157X-RAY DIFFRACTION99.9565
4.197-4.5970.2251320.1511996X-RAY DIFFRACTION100
4.597-5.1390.2251220.1611826X-RAY DIFFRACTION99.8974
5.139-5.9320.2451060.1941610X-RAY DIFFRACTION100
5.932-7.2610.262920.1921381X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1051-0.01760.04390.452-0.41120.77390.0102-0.0152-0.0039-0.0491-0.0403-0.0359-0.05740.14790.03020.0382-0.0287-0.0120.04060.00890.056811.979920.664216.1828
20.0631-0.01160.01560.76660.54521.1118-0.02330.0341-0.02860.0741-0.04290.1148-0.1306-0.15960.06620.06210.0320.03530.05870.00020.0732-15.09434.679-18.2161
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA10 - 479
2X-RAY DIFFRACTION2ALLB11 - 479

+
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