[English] 日本語
Yorodumi
- PDB-1mvn: PPC decarboxylase mutant C175S complexed with pantothenoylaminoet... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mvn
TitlePPC decarboxylase mutant C175S complexed with pantothenoylaminoethenethiol
ComponentsPPC decarboxylase AtHAL3a
KeywordsLYASE / Flavoprotein / PPC decarboxylase / active site mutant C175S / complexed with ene-thiol reaction intermediate
Function / homology
Function and homology information


phosphopantothenoylcysteine decarboxylase / phosphopantothenoylcysteine decarboxylase activity / hyperosmotic salinity response / coenzyme A biosynthetic process
Similarity search - Function
Flavin prenyltransferase-like / Flavoprotein / Flavin prenyltransferase-like / Flavoprotein / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Chem-PCO / Phosphopantothenoylcysteine decarboxylase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.21 Å
AuthorsSteinbacher, S. / Hernandez-Acosta, P. / Bieseler, B. / Blaesse, M. / Huber, R. / Culianez-Macia, F.A. / Kupke, T.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Crystal Structure of the Plant PPC Decarboxylase AtHAL3a Complexed with an Ene-thiol Reaction Intermediate
Authors: Steinbacher, S. / Hernandez-Acosta, P. / Bieseler, B. / Blaesse, M. / Huber, R. / Culianez-Macia, F.A. / Kupke, T.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Arabidopsis thaliana flavoprotein AtHAL3a catalyzes the decarboxylation of 4'-phosphopantothenoylcysteine to 4'-phosphopantetheine, a key step in coenzyme A biosynthesis
Authors: Kupke, T. / Hernandez-Acosta, P. / Steinbacher, S. / Culianez-Macia, F.A.
#2: Journal: J.Biol.Chem. / Year: 2002
Title: Molecular characterization of the Arabidopsis thaliana flavoprotein AtHAL3a reveals the general reaction mechanism of 4'-phosphopantothenoylcysteine decarboxylases
Authors: Hernandez-Acosta, P. / Schmid, D.G. / Jung, G. / Culianez-Macia, F.A. / Kupke, T.
#3: Journal: Plant J. / Year: 1999
Title: Arabidopsis thaliana AtHal3: a flavoprotein related to salt and osmotic tolerance and plant growth
Authors: Espinosa-Ruiz, A. / Belles, J.M. / Serrano, R. / Culianez-Macia, F.A.
#4: Journal: Structure / Year: 2000
Title: The X-ray structure of the FMN-binding protein AtHal3 provides the structural basis for the activity of a regulatory subunit involved in signal transduction
Authors: Albert, A. / Martinez-Ripoll, M. / Espinosa-Ruiz, A. / Yenush, L. / Culianez-Macia, F.A. / Serrano, R.
History
DepositionSep 26, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 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: PPC decarboxylase AtHAL3a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0973
Polymers23,3651
Non-polymers7332
Water75742
1
A: PPC decarboxylase AtHAL3a
hetero molecules

A: PPC decarboxylase AtHAL3a
hetero molecules

A: PPC decarboxylase AtHAL3a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2929
Polymers70,0943
Non-polymers2,1986
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area11000 Å2
ΔGint-65 kcal/mol
Surface area20920 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)111.181, 111.181, 33.450
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by the three-fold axis

-
Components

#1: Protein PPC decarboxylase AtHAL3a / Halotolerance protein Hal3a


Mass: 23364.775 Da / Num. of mol.: 1 / Mutation: C175S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9SWE5, phosphopantothenoylcysteine decarboxylase
#2: Chemical ChemComp-PCO / 2,4-DIHYDROXY-N-[2-(2-MERCAPTO-VINYLCARBAMOYL)-ETHYL]-3,3-DIMETHYL-BUTYRAMIDE / PANTOTHENOYLAMINOETHENETHIOL


Mass: 276.353 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20N2O4S
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.8 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: ammonium sulphate, imidazole, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
220 mMTris-HCl1droppH7.5
31.4 Mammonium sulfate1reservoir
4100 mMimidazole-HCl1reservoirpH6.3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 3, 2002 / Details: mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.21→20 Å / Num. all: 11729 / Num. obs: 11729 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 22
Reflection shellResolution: 2.21→2.29 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 3.1 / Num. unique all: 1012 / % possible all: 84.5
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 84.5 %

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
CNS1.1phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1MVL

1mvl


Resolution: 2.21→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 602 -random
Rwork0.2105 ---
all0.2196 11724 --
obs0.2196 11724 95.3 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.756 Å2-0.406 Å20 Å2
2--6.756 Å20 Å2
3----13.511 Å2
Refinement stepCycle: LAST / Resolution: 2.21→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1433 0 49 42 1524
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_d0.011
X-RAY DIFFRACTIONc_angle_deg1.38
X-RAY DIFFRACTIONc_mcbond_it2.491.5
X-RAY DIFFRACTIONc_mcangle_it3.7872
X-RAY DIFFRACTIONc_scbond_it4.0732
X-RAY DIFFRACTIONc_scangle_it5.2113
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2fmn.paramfmn.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5pco.parampco.top
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor Rwork: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_d

+
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