[English] 日本語
Yorodumi
- PDB-7ae7: Structure of Sedimentibacter hydroxybenzoicus vanillic acid decar... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ae7
TitleStructure of Sedimentibacter hydroxybenzoicus vanillic acid decarboxylase (ShVdcCD) in open form, with truncated ShVdcD (V59X)
Components
  • Phenolic acid decarboxylase
  • Protein ShdD
KeywordsLYASE / Decarboxylase / Hetero-complex / UbiD
Function / homology
Function and homology information


4-hydroxybenzoate decarboxylase / protocatechuate decarboxylase / 4-hydroxybenzoate decarboxylase activity / protocatechuate decarboxylase activity / ferulate metabolic process / cinnamic acid catabolic process / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity / ubiquinone biosynthetic process / : / response to toxic substance ...4-hydroxybenzoate decarboxylase / protocatechuate decarboxylase / 4-hydroxybenzoate decarboxylase activity / protocatechuate decarboxylase activity / ferulate metabolic process / cinnamic acid catabolic process / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity / ubiquinone biosynthetic process / : / response to toxic substance / metal ion binding / cytosol
Similarity search - Function
Phenolic acid decarboxylase subunit C / : / : / : / : / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase N-terminal domain / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase C-terminal domain / UbiD decarboxylyase family / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Rift-related domain
Similarity search - Domain/homology
Protein ShdD / Phenolic acid decarboxylase
Similarity search - Component
Biological speciesSedimentibacter hydroxybenzoicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsMarshall, S.A. / Leys, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: To Be Published
Title: Domain mobility and allosteric activation of UbiD decarboxylases
Authors: Marshall, S.A. / Payne, K.A.P. / Leys, D.
History
DepositionSep 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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: Phenolic acid decarboxylase
B: Phenolic acid decarboxylase
C: Phenolic acid decarboxylase
D: Phenolic acid decarboxylase
E: Phenolic acid decarboxylase
F: Phenolic acid decarboxylase
a: Protein ShdD
b: Protein ShdD
c: Protein ShdD
d: Protein ShdD
e: Protein ShdD
f: Protein ShdD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)364,91923
Polymers364,41112
Non-polymers50711
Water9,656536
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43650 Å2
ΔGint-424 kcal/mol
Surface area103110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.553, 200.945, 201.991
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Protein
Phenolic acid decarboxylase / PAD / 3 / 4-dihydroxybenzoate decarboxylase / 4-dihydroxybenzoate DC / 4-hydroxybenzoate ...PAD / 3 / 4-dihydroxybenzoate decarboxylase / 4-dihydroxybenzoate DC / 4-hydroxybenzoate decarboxylase / 4-hydroxybenzoate DC / Phenolic acid decarboxylase subunit C


Mass: 54020.457 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sedimentibacter hydroxybenzoicus (bacteria)
Gene: shdC, ohb1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9S4M7, protocatechuate decarboxylase, 4-hydroxybenzoate decarboxylase
#2: Protein
Protein ShdD / Phenolic acid decarboxylase subunit D / PAD


Mass: 6714.751 Da / Num. of mol.: 6 / Mutation: V59X
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sedimentibacter hydroxybenzoicus (bacteria)
Gene: shdD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4R102
#3: Chemical
ChemComp-NA / SODIUM ION / Phenolic acid decarboxylase subunit D / PAD


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.13 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: JCSG-Plus B8 (0.2 M Magnesium chloride hexahydrate, 0.1 M Tris, pH7, 10% PEG 8000

-
Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.66→71.43 Å / Num. obs: 119314 / % possible obs: 99.85 % / Redundancy: 21.5 % / Biso Wilson estimate: 37.28 Å2 / CC1/2: 0.988 / Net I/σ(I): 8.25
Reflection shellResolution: 2.66→2.755 Å / Mean I/σ(I) obs: 2.79 / Num. unique obs: 11673 / CC1/2: 0.618

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M1C

5m1c


Resolution: 2.66→71.42 Å / SU ML: 0.3163 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 21.6923
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2268 5824 4.89 %
Rwork0.1799 113353 -
obs0.1822 119177 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.55 Å2
Refinement stepCycle: LAST / Resolution: 2.66→71.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23802 0 11 536 24349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00324386
X-RAY DIFFRACTIONf_angle_d0.662233350
X-RAY DIFFRACTIONf_chiral_restr0.053807
X-RAY DIFFRACTIONf_plane_restr0.00564365
X-RAY DIFFRACTIONf_dihedral_angle_d5.0143366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.690.38371690.28853199X-RAY DIFFRACTION85.35
2.69-2.720.32561840.26763780X-RAY DIFFRACTION100
2.72-2.750.27741580.24083797X-RAY DIFFRACTION100
2.75-2.780.2931970.22763726X-RAY DIFFRACTION100
2.78-2.820.27831760.22633813X-RAY DIFFRACTION100
2.82-2.860.28462080.22463691X-RAY DIFFRACTION100
2.86-2.90.29541920.22783797X-RAY DIFFRACTION100
2.9-2.940.28371910.22253728X-RAY DIFFRACTION100
2.94-2.990.24971960.21473779X-RAY DIFFRACTION100
2.99-3.040.28992170.21143727X-RAY DIFFRACTION99.97
3.04-3.090.28441970.20723784X-RAY DIFFRACTION100
3.09-3.150.25122230.19073719X-RAY DIFFRACTION100
3.15-3.210.24542100.19363749X-RAY DIFFRACTION100
3.21-3.270.26121690.20063816X-RAY DIFFRACTION100
3.27-3.350.24161630.19753772X-RAY DIFFRACTION100
3.35-3.420.25211920.19313800X-RAY DIFFRACTION100
3.42-3.510.23622140.19083773X-RAY DIFFRACTION100
3.51-3.60.24762000.18483769X-RAY DIFFRACTION100
3.6-3.710.23642010.17693777X-RAY DIFFRACTION100
3.71-3.830.20371770.16243810X-RAY DIFFRACTION100
3.83-3.970.2092170.15123779X-RAY DIFFRACTION100
3.97-4.120.19051720.14393822X-RAY DIFFRACTION100
4.12-4.310.1861730.13853818X-RAY DIFFRACTION100
4.31-4.540.17822140.13663792X-RAY DIFFRACTION100
4.54-4.820.16491960.14243845X-RAY DIFFRACTION100
4.82-5.20.19721850.14923829X-RAY DIFFRACTION100
5.2-5.720.22322230.16813833X-RAY DIFFRACTION100
5.72-6.550.21022020.17863855X-RAY DIFFRACTION100
6.55-8.250.20641960.17053923X-RAY DIFFRACTION100
8.25-71.420.1722120.17464051X-RAY DIFFRACTION98.98
Refinement TLS params.Method: refined / Origin x: -31.0540171644 Å / Origin y: 24.2582848945 Å / Origin z: -43.0570647466 Å
111213212223313233
T0.186477443939 Å20.0337810866907 Å2-0.0172817823457 Å2-0.201123063655 Å2-0.0194749182089 Å2--0.187270162388 Å2
L0.355693165841 °20.0202083998698 °20.0278461156091 °2-0.285728861586 °20.0123204134738 °2--0.355616280718 °2
S0.0332653567817 Å °0.0505335915716 Å °-0.0351183566803 Å °-0.0811406074911 Å °-0.041502907031 Å °-0.0359588190867 Å °0.0638571831181 Å °0.0733863075381 Å °0.00870679340179 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://pdbjlvh1.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