[English] 日本語
Yorodumi
- PDB-9iz3: Crystal structure of phosphonopyruvate decarboxylase RhiEF from B... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9iz3
TitleCrystal structure of phosphonopyruvate decarboxylase RhiEF from Bacillus subtilis ATCC6633
Components
  • Putative phosphonopyruvate decarboxylase alpha subunit
  • Putative phosphonopyruvate decarboxylase beta subunit
KeywordsLYASE / phosphonopyruvate decarboxylase / RhiEF / rhizocticin biosynthesis / thiamine pyrophosphate
Function / homology
Function and homology information


carboxy-lyase activity / thiamine pyrophosphate binding / magnesium ion binding
Similarity search - Function
: / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate-binding fold
Similarity search - Domain/homology
Putative phosphonopyruvate decarboxylase alpha subunit / Putative phosphonopyruvate decarboxylase beta subunit
Similarity search - Component
Biological speciesBacillus spizizenii ATCC 6633 = JCM 2499 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.46 Å
AuthorsNakamura, A. / Kojima, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochemistry / Year: 2024
Title: Structural Analysis of Phosphonopyruvate Decarboxylase RhiEF: First Insights into an Ancestral Heterooligomeric Thiamine Pyrophosphate-Dependent Decarboxylase.
Authors: Nakamura, A. / Shiina, A. / Fukaya, T. / Seki, Y. / Momiyama, M. / Kojima, S.
History
DepositionJul 31, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative phosphonopyruvate decarboxylase alpha subunit
B: Putative phosphonopyruvate decarboxylase beta subunit
C: Putative phosphonopyruvate decarboxylase alpha subunit
D: Putative phosphonopyruvate decarboxylase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,49211
Polymers81,8194
Non-polymers6727
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9130 Å2
ΔGint-178 kcal/mol
Surface area25730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.991, 176.991, 68.600
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

-
Components

#1: Protein Putative phosphonopyruvate decarboxylase alpha subunit


Mass: 20342.178 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus spizizenii ATCC 6633 = JCM 2499 (bacteria)
Gene: rhiE / Production host: Escherichia coli (E. coli) / References: UniProt: D4HRI2
#2: Protein Putative phosphonopyruvate decarboxylase beta subunit


Mass: 20567.533 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus spizizenii ATCC 6633 = JCM 2499 (bacteria)
Gene: rhiF / Production host: Escherichia coli (E. coli) / References: UniProt: D4HRI3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.79 Å3/Da / Density % sol: 67.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 1.3M ammonium sulfate, 0.1M sodium citrate, 4% v/v tert-butanol

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.46→44.26 Å / Num. obs: 44917 / % possible obs: 99.8 % / Redundancy: 10.3 % / Biso Wilson estimate: 59.61 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.026 / Rsym value: 0.081 / Net I/σ(I): 18
Reflection shellResolution: 2.46→2.55 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 2 / Num. unique obs: 4670 / CC1/2: 0.785 / Rpim(I) all: 0.47 / Rsym value: 1.464 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.46→40.98 Å / SU ML: 0.3432 / Cross valid method: FREE R-VALUE / σ(F): 1.28 / Phase error: 32.1866 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2717 2225 4.96 %
Rwork0.2395 42664 -
obs0.2412 44889 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 99.52 Å2
Refinement stepCycle: LAST / Resolution: 2.46→40.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4939 0 35 10 4984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00555055
X-RAY DIFFRACTIONf_angle_d0.85956845
X-RAY DIFFRACTIONf_chiral_restr0.0508793
X-RAY DIFFRACTIONf_plane_restr0.0062865
X-RAY DIFFRACTIONf_dihedral_angle_d8.12213017
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.510.32771210.30712655X-RAY DIFFRACTION99.71
2.51-2.570.34061200.29752663X-RAY DIFFRACTION99.75
2.57-2.640.33961380.29972673X-RAY DIFFRACTION99.57
2.64-2.710.34781260.31852606X-RAY DIFFRACTION99.71
2.71-2.790.3431550.30722609X-RAY DIFFRACTION99.6
2.79-2.880.37531230.30712681X-RAY DIFFRACTION99.75
2.88-2.980.31451390.28862673X-RAY DIFFRACTION99.72
2.98-3.10.27411290.2652650X-RAY DIFFRACTION99.82
3.1-3.240.29881450.28222653X-RAY DIFFRACTION99.79
3.24-3.410.28231530.26042619X-RAY DIFFRACTION99.64
3.41-3.620.30561560.25832660X-RAY DIFFRACTION99.96
3.62-3.90.26621420.24842654X-RAY DIFFRACTION99.96
3.9-4.30.21711430.21622695X-RAY DIFFRACTION99.96
4.3-4.920.24041660.18622663X-RAY DIFFRACTION99.89
4.92-6.190.28581190.23492721X-RAY DIFFRACTION99.93
6.19-40.980.24591500.21072789X-RAY DIFFRACTION99.69
Refinement TLS params.Method: refined / Origin x: 63.8904344061 Å / Origin y: 67.3865767422 Å / Origin z: 23.036848746 Å
111213212223313233
T0.147045663149 Å20.358037841591 Å20.117441488902 Å2-0.777490744818 Å2-0.00871894719439 Å2--0.349716624786 Å2
L0.127203029221 °2-0.0442395846625 °2-0.0433694773265 °2-0.133656515095 °20.0982497005443 °2--0.0782843817588 °2
S-0.0959196553949 Å °-0.129750224803 Å °-0.110448182066 Å °-0.0741435108892 Å °0.207819883071 Å °-0.0950987313841 Å °0.13258363452 Å °0.303460938973 Å °0.101837953506 Å °
Refinement TLS groupSelection details: all

+
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