[English] 日本語
Yorodumi
- PDB-5msd: Structure of the A domain of carboxylic acid reductase (CAR) from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5msd
TitleStructure of the A domain of carboxylic acid reductase (CAR) from Nocardia iowensis in complex with AMP and benzoic acid
ComponentsCarboxylic acid reductase
KeywordsOXIDOREDUCTASE / adenylation domain / carboxylic acid reductase
Function / homology
Function and homology information


carboxylate reductase (NADP+) / aryl-aldehyde dehydrogenase (NADP+) activity / long-chain fatty acid-CoA ligase activity / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / biosynthetic process / phosphopantetheine binding / NADP binding / ATP binding / membrane
Similarity search - Function
Carboxylic acid reductase / Thioester reductase-like domain / Fatty acyl-coenzyme A reductase, NAD-binding domain / Male sterility protein / ANL, N-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / Polyketide synthase, phosphopantetheine-binding domain ...Carboxylic acid reductase / Thioester reductase-like domain / Fatty acyl-coenzyme A reductase, NAD-binding domain / Male sterility protein / ANL, N-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Short-chain dehydrogenases/reductases family signature. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / BENZOIC ACID / Carboxylic acid reductase
Similarity search - Component
Biological speciesNocardia iowensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsDunstan, M.S. / Leys, D.
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Structures of carboxylic acid reductase reveal domain dynamics underlying catalysis.
Authors: Gahloth, D. / Dunstan, M.S. / Quaglia, D. / Klumbys, E. / Lockhart-Cairns, M.P. / Hill, A.M. / Derrington, S.R. / Scrutton, N.S. / Turner, N.J. / Leys, D.
History
DepositionJan 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.2Jul 26, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.3Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.5Jan 17, 2024Group: 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: Carboxylic acid reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,9493
Polymers128,4801
Non-polymers4692
Water10,629590
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint3 kcal/mol
Surface area26490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.650, 54.499, 66.365
Angle α, β, γ (deg.)93.37, 97.68, 102.44
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Carboxylic acid reductase / CAR / ATP/NADPH-dependent carboxylic acid reductase / Aryl aldehyde oxidoreductase


Mass: 128479.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardia iowensis (bacteria) / Gene: car / Production host: Escherichia coli (E. coli)
References: UniProt: Q6RKB1, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor, carboxylate reductase (NADP+)
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 590 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: Crystals of A domain CARni (30mg/ml) were obtained using the sitting-drop vapour-diffusion and grew within 7 days at 4 degrees in 0.12 M ethylene glycols 0.1 M Tris-Bicine pH 8.5 30% glycerol/PEG 4K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.71→29.061 Å / Num. obs: 63656 / % possible obs: 95 % / Redundancy: 2.1 % / CC1/2: 1 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.1

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MSC

5msc


Resolution: 1.71→29.061 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 24.72
RfactorNum. reflection% reflection
Rfree0.2146 3195 5.02 %
Rwork0.1802 --
obs0.1818 63652 82.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.71→29.061 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4932 0 32 590 5554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085062
X-RAY DIFFRACTIONf_angle_d1.2016889
X-RAY DIFFRACTIONf_dihedral_angle_d13.6331875
X-RAY DIFFRACTIONf_chiral_restr0.041788
X-RAY DIFFRACTIONf_plane_restr0.006907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7096-1.73520.4206560.33631050X-RAY DIFFRACTION33
1.7352-1.76230.3456620.31931228X-RAY DIFFRACTION38
1.7623-1.79120.3935780.29281371X-RAY DIFFRACTION44
1.7912-1.8220.3082860.28241590X-RAY DIFFRACTION50
1.822-1.85520.30241060.261749X-RAY DIFFRACTION56
1.8552-1.89080.28131050.24882062X-RAY DIFFRACTION64
1.8908-1.92940.25981160.2372364X-RAY DIFFRACTION75
1.9294-1.97140.26381840.22262830X-RAY DIFFRACTION90
1.9714-2.01720.26241550.20672983X-RAY DIFFRACTION93
2.0172-2.06760.25021210.20963030X-RAY DIFFRACTION95
2.0676-2.12350.21831870.19983055X-RAY DIFFRACTION97
2.1235-2.1860.21261720.19623085X-RAY DIFFRACTION97
2.186-2.25650.25241670.19313100X-RAY DIFFRACTION97
2.2565-2.33720.21691650.18513037X-RAY DIFFRACTION97
2.3372-2.43070.21941770.1963068X-RAY DIFFRACTION97
2.4307-2.54120.22871740.193101X-RAY DIFFRACTION98
2.5412-2.67510.2241540.19093116X-RAY DIFFRACTION97
2.6751-2.84260.21621630.19493082X-RAY DIFFRACTION98
2.8426-3.06190.22691600.19273129X-RAY DIFFRACTION98
3.0619-3.36960.21761380.17663095X-RAY DIFFRACTION97
3.3696-3.85620.18781460.15563132X-RAY DIFFRACTION98
3.8562-4.85480.17071530.14053121X-RAY DIFFRACTION98
4.8548-29.06540.1921700.16063079X-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