[English] 日本語
Yorodumi
- PDB-6c4n: Pseudopaline dehydrogenase (PaODH) - NADP+ bound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6c4n
TitlePseudopaline dehydrogenase (PaODH) - NADP+ bound
ComponentsPseudopaline dehydrogenase
KeywordsOXIDOREDUCTASE / Opine Dehydrogenase Metallophore Siderophore Yersinopine Pseudopaline Staphylopine
Function / homologyOxidoreductases; Acting on the CH-NH group of donors; With NAD+ or NADP+ as acceptor / Opine metallophore dehydrogenase / Staphylopine dehydrogenase / oxidoreductase activity / NAD(P)-binding domain superfamily / plasma membrane / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Pseudopaline synthase
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMcFarlane, J.S. / Davis, C.L. / Lamb, A.L.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE1403293 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008545 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103418 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Staphylopine, pseudopaline, and yersinopine dehydrogenases: A structural and kinetic analysis of a new functional class of opine dehydrogenase.
Authors: McFarlane, J.S. / Davis, C.L. / Lamb, A.L.
History
DepositionJan 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.journal_abbrev ..._chem_comp.name / _citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 2.0Jun 6, 2018Group: Atomic model / Data collection / Database references / Category: atom_site / citation
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 2.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Oct 4, 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: Pseudopaline dehydrogenase
B: Pseudopaline dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7065
Polymers99,1572
Non-polymers1,5493
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-26 kcal/mol
Surface area34500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.046, 53.634, 96.756
Angle α, β, γ (deg.)90.00, 99.03, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-788-

HOH

-
Components

#1: Protein Pseudopaline dehydrogenase


Mass: 49578.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA4835 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HUX5
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / 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: 2.45 Å3/Da / Density % sol: 49.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 100 mM BisTris pH 5.45, 200 mM ammonium acetate, 26% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→39.5 Å / Num. obs: 64916 / % possible obs: 97.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.4
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 0.777 / Num. unique obs: 4435

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6C4L

6c4l


Resolution: 1.95→38.17 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.211 1998 3.08 %
Rwork0.168 --
obs0.169 64880 96.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→38.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6540 0 100 397 7037
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016812
X-RAY DIFFRACTIONf_angle_d1.1419286
X-RAY DIFFRACTIONf_dihedral_angle_d18.0494051
X-RAY DIFFRACTIONf_chiral_restr0.0811022
X-RAY DIFFRACTIONf_plane_restr0.0081210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9482-1.99690.30781380.22894356X-RAY DIFFRACTION94
1.9969-2.05090.23671390.20334355X-RAY DIFFRACTION95
2.0509-2.11130.26991370.19874358X-RAY DIFFRACTION95
2.1113-2.17940.22591440.17854505X-RAY DIFFRACTION97
2.1794-2.25730.21171440.17044529X-RAY DIFFRACTION98
2.2573-2.34770.22321440.17314527X-RAY DIFFRACTION98
2.3477-2.45450.24041420.17234486X-RAY DIFFRACTION97
2.4545-2.58390.2431380.17214372X-RAY DIFFRACTION95
2.5839-2.74570.20651450.16344542X-RAY DIFFRACTION98
2.7457-2.95760.22431450.17054569X-RAY DIFFRACTION98
2.9576-3.25510.20781420.17554431X-RAY DIFFRACTION96
3.2551-3.72580.21031460.1664616X-RAY DIFFRACTION99
3.7258-4.69280.17481450.14154581X-RAY DIFFRACTION98
4.6928-38.17760.18581490.16344655X-RAY DIFFRACTION97

+
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