[English] 日本語
Yorodumi
- PDB-5dbv: Structure of a C269A mutant of propionaldehyde dehydrogenase from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5dbv
TitleStructure of a C269A mutant of propionaldehyde dehydrogenase from the Clostridium phytofermentans fucose utilisation bacterial microcompartment
ComponentsAldehyde Dehydrogenase
KeywordsOXIDOREDUCTASE / Acylating aldehyde dehydrogenase / CoA / propionaldehyde / BMC
Function / homology
Function and homology information


acetaldehyde dehydrogenase (acetylating) activity / nucleotide binding
Similarity search - Function
Acetaldehyde/propionaldehyde dehydrogenase, EutE/PduP-related / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase ...Acetaldehyde/propionaldehyde dehydrogenase, EutE/PduP-related / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / COENZYME A / Aldehyde Dehydrogenase
Similarity search - Component
Biological speciesClostridium phytofermentans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsTuck, L.R. / Altenbach, K. / Ang, T.F. / Crawshaw, A.D. / Campopiano, D.J. / Clarke, D.J. / Marles-Wright, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M010996/1 United Kingdom
CitationJournal: Sci Rep / Year: 2016
Title: Insight into Coenzyme A cofactor binding and the mechanism of acyl-transfer in an acylating aldehyde dehydrogenase from Clostridium phytofermentans.
Authors: Tuck, L.R. / Altenbach, K. / Ang, T.F. / Crawshaw, A.D. / Campopiano, D.J. / Clarke, D.J. / Marles-Wright, J.
History
DepositionAug 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 10, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aldehyde Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9579
Polymers47,6651
Non-polymers1,2928
Water5,278293
1
A: Aldehyde Dehydrogenase
hetero molecules

A: Aldehyde Dehydrogenase
hetero molecules

A: Aldehyde Dehydrogenase
hetero molecules

A: Aldehyde Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,82736
Polymers190,6594
Non-polymers5,16832
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area25990 Å2
ΔGint-184 kcal/mol
Surface area54630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.264, 138.264, 84.445
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-504-

ACT

21A-504-

ACT

31A-840-

HOH

41A-878-

HOH

-
Components

#1: Protein Aldehyde Dehydrogenase


Mass: 47664.781 Da / Num. of mol.: 1 / Fragment: UNP residues 20-462 / Mutation: C269A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium phytofermentans (strain ATCC 700394 / DSM 18823 / ISDg) (bacteria)
Gene: Cphy_1178 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9KN57
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 42.05 % / Description: Square bipyramid
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PROTEIN IN 50 MM TRIS.HCL, PH 8.0, 35 MM NACL. 1:1 HANGING DROPS OVER: 0.1 M SODIUM ACETATE, PH 4.5 - 4.8 1.4 - 1.8 M AMMONIUM SULPHATE. Crystals soaked with 10 mM CoA in well solution.
PH range: 4.5 - 4.8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2015
RadiationMonochromator: Single Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.77→49.89 Å / Num. all: 40079 / Num. obs: 40079 / % possible obs: 99.9 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.073 / Rsym value: 0.079 / Net I/σ(I): 22.4
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 11.4 % / Rmerge(I) obs: 1.05 / Mean I/σ(I) obs: 2.3 / % possible all: 98.5

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C3S

4c3s


Resolution: 1.77→48.89 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.183 2016 5.03 %Random selection
Rwork0.1465 ---
obs0.1484 40064 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.9 Å2
Refinement stepCycle: LAST / Resolution: 1.77→48.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3220 0 79 293 3592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013344
X-RAY DIFFRACTIONf_angle_d1.2634528
X-RAY DIFFRACTIONf_dihedral_angle_d14.5631245
X-RAY DIFFRACTIONf_chiral_restr0.052531
X-RAY DIFFRACTIONf_plane_restr0.007581
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7681-1.81230.26131440.21612625X-RAY DIFFRACTION99
1.8123-1.86130.24591250.19672722X-RAY DIFFRACTION100
1.8613-1.91610.22811240.1812684X-RAY DIFFRACTION100
1.9161-1.97790.24171610.16892677X-RAY DIFFRACTION100
1.9779-2.04860.21791370.15862705X-RAY DIFFRACTION100
2.0486-2.13060.17341440.14492693X-RAY DIFFRACTION100
2.1306-2.22760.17741310.14362711X-RAY DIFFRACTION100
2.2276-2.34510.20531270.14122713X-RAY DIFFRACTION100
2.3451-2.4920.19051630.14522678X-RAY DIFFRACTION100
2.492-2.68440.22611530.15082702X-RAY DIFFRACTION100
2.6844-2.95450.18971490.15252738X-RAY DIFFRACTION100
2.9545-3.38190.18661510.15342732X-RAY DIFFRACTION100
3.3819-4.26050.13911460.12482777X-RAY DIFFRACTION100
4.2605-48.90240.16311610.13842891X-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)
13.16010.9552-0.73512.0763-0.46051.35690.1694-0.23940.05080.302-0.1414-0.0456-0.26080.0785-0.0140.3222-0.02430.00690.2841-0.03410.1651-11.356115.96823.7955
21.66790.6354-1.03130.7366-0.57191.64650.1128-0.2062-0.03920.1734-0.11570.0077-0.13980.03130.00840.2249-0.01260.01170.20460.01050.2105-11.130511.85216.281
34.9775-0.3032-0.06172.20450.31374.0110.0881-0.03080.15050.1522-0.02960.2339-0.2708-0.3786-0.01690.2460.01970.08590.1306-0.00490.2361-18.341324.482516.0407
41.77091.0396-0.20571.4395-0.22981.2403-0.0125-0.01210.00770.10360.03450.1646-0.0243-0.1686-0.07150.17550.01630.03290.22180.00740.2495-27.2065-0.343510.4993
51.6408-0.3057-0.37830.7955-0.33771.8851-0.0281-0.0179-0.15490.07380.04350.20950.0195-0.39980.03580.2012-0.01950.0310.34090.0280.3133-37.5534-6.370711.2994
62.51480.8753-0.99851.1762-0.45221.2145-0.00780.0603-0.04060.02090.0201-0.0464-0.0495-0.0131-0.01250.19660.0126-0.00920.17940.01980.1943-9.96535.04725.0078
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 87 )
2X-RAY DIFFRACTION2chain 'A' and (resid 88 through 183 )
3X-RAY DIFFRACTION3chain 'A' and (resid 184 through 218 )
4X-RAY DIFFRACTION4chain 'A' and (resid 219 through 271 )
5X-RAY DIFFRACTION5chain 'A' and (resid 272 through 406 )
6X-RAY DIFFRACTION6chain 'A' and (resid 407 through 462 )

+
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