[English] 日本語
Yorodumi
- PDB-5jfl: Crystal structure of Rhodopseudomonas palustris propionaldehyde d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jfl
TitleCrystal structure of Rhodopseudomonas palustris propionaldehyde dehydrogenase with bound NAD+
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / acylating aldehyde dehydrogenase / propionylcysteine / bacterial microcompartments
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Aldehyde dehydrogenase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZarzycki, J. / Sutter, M. / Kerfeld, C.A.
CitationJournal: Sci Rep / Year: 2017
Title: In Vitro Characterization and Concerted Function of Three Core Enzymes of a Glycyl Radical Enzyme - Associated Bacterial Microcompartment.
Authors: Zarzycki, J. / Sutter, M. / Cortina, N.S. / Erb, T.J. / Kerfeld, C.A.
History
DepositionApr 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
C: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase
E: Aldehyde dehydrogenase
F: Aldehyde dehydrogenase
G: Aldehyde dehydrogenase
H: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)449,49616
Polymers444,1888
Non-polymers5,3078
Water16,538918
1
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
C: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,7488
Polymers222,0944
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20200 Å2
ΔGint-71 kcal/mol
Surface area54810 Å2
MethodPISA
2
E: Aldehyde dehydrogenase
F: Aldehyde dehydrogenase
G: Aldehyde dehydrogenase
H: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,7488
Polymers222,0944
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20100 Å2
ΔGint-73 kcal/mol
Surface area54580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.393, 154.796, 126.594
Angle α, β, γ (deg.)90.00, 90.13, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Aldehyde dehydrogenase /


Mass: 55523.531 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (strain BisB18) (phototrophic)
Strain: BisB18 / Gene: RPC_1174 / Production host: Escherichia coli (E. coli) / References: UniProt: Q21A49
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 918 / 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: 2.37 Å3/Da / Density % sol: 48.08 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 50 mM sodium citrate, pH 4.8, 4% w/v PEG8000, 5 mM NAD+

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00001 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.3→33.643 Å / Num. obs: 357425 / % possible obs: 98.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 10.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.868 / Mean I/σ(I) obs: 2.7 / % possible all: 98

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C3S

4c3s


Resolution: 2.3→33.643 Å / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 36.16 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2282 4003 1.12 %
Rwork0.1885 --
obs0.1896 357425 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→33.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26378 0 352 918 27648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00427148
X-RAY DIFFRACTIONf_angle_d0.61336885
X-RAY DIFFRACTIONf_dihedral_angle_d14.56116520
X-RAY DIFFRACTIONf_chiral_restr0.0444445
X-RAY DIFFRACTIONf_plane_restr0.0044730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3002-2.33980.32591940.294217427X-RAY DIFFRACTION96
2.3398-2.38240.30191960.276617502X-RAY DIFFRACTION97
2.3824-2.42810.30191890.274917427X-RAY DIFFRACTION97
2.4281-2.47770.30331990.259917542X-RAY DIFFRACTION97
2.4777-2.53150.34271970.25817557X-RAY DIFFRACTION97
2.5315-2.59030.30142000.253217523X-RAY DIFFRACTION97
2.5903-2.65510.29441930.250117607X-RAY DIFFRACTION97
2.6551-2.72680.31281990.245817681X-RAY DIFFRACTION97
2.7268-2.8070.24072040.231317637X-RAY DIFFRACTION98
2.807-2.89750.3071920.232917756X-RAY DIFFRACTION98
2.8975-3.00090.23611980.228517684X-RAY DIFFRACTION98
3.0009-3.12090.3261870.214117728X-RAY DIFFRACTION98
3.1209-3.26270.22452000.200617756X-RAY DIFFRACTION98
3.2627-3.43440.22112000.19217723X-RAY DIFFRACTION98
3.4344-3.6490.23611980.177417725X-RAY DIFFRACTION98
3.649-3.930.18252010.165217798X-RAY DIFFRACTION98
3.93-4.3240.18151920.148317772X-RAY DIFFRACTION98
4.324-4.94640.20111980.132717673X-RAY DIFFRACTION98
4.9464-6.21920.18652020.154817864X-RAY DIFFRACTION99
6.2192-26.91440.14772040.132417915X-RAY DIFFRACTION99

+
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