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- PDB-5msc: Structure of the A domain of carboxylic acid reductase (CAR) from... -

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Basic information

Entry
Database: PDB / ID: 5msc
TitleStructure of the A domain of carboxylic acid reductase (CAR) from Nocardia iowensis in complex with AMP
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 / Carboxylic acid reductase
Similarity search - Component
Biological speciesNocardia iowensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 1.5May 8, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carboxylic acid reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,8272
Polymers128,4801
Non-polymers3471
Water6,720373
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-2 kcal/mol
Surface area26900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.080, 54.250, 66.240
Angle α, β, γ (deg.)93.51, 98.82, 101.78
Int Tables number1
Space group name H-MP1

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.976 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: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.85→43.52 Å / Num. obs: 59592 / % possible obs: 96.4 % / Redundancy: 3.4 % / CC1/2: 1 / Net I/σ(I): 12.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_120002932

Resolution: 1.85→43.52 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.43
RfactorNum. reflection% reflection
Rfree0.2551 2857 4.97 %
Rwork0.2129 --
obs0.2149 57435 96.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→43.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4924 0 23 373 5320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095054
X-RAY DIFFRACTIONf_angle_d1.2816881
X-RAY DIFFRACTIONf_dihedral_angle_d13.8071874
X-RAY DIFFRACTIONf_chiral_restr0.049788
X-RAY DIFFRACTIONf_plane_restr0.006905
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.88190.38151300.32132390X-RAY DIFFRACTION85
1.8819-1.91620.39271210.28412680X-RAY DIFFRACTION94
1.9162-1.9530.31751580.27372678X-RAY DIFFRACTION96
1.953-1.99290.34151500.26742731X-RAY DIFFRACTION97
1.9929-2.03620.26911580.25782697X-RAY DIFFRACTION97
2.0362-2.08360.2851440.24622811X-RAY DIFFRACTION97
2.0836-2.13570.28791470.2372693X-RAY DIFFRACTION97
2.1357-2.19340.26331420.23662777X-RAY DIFFRACTION97
2.1934-2.2580.28331510.23122788X-RAY DIFFRACTION97
2.258-2.33080.31051570.23212693X-RAY DIFFRACTION97
2.3308-2.41410.28361400.23942776X-RAY DIFFRACTION98
2.4141-2.51080.23821420.23632800X-RAY DIFFRACTION98
2.5108-2.6250.27511460.23482764X-RAY DIFFRACTION98
2.625-2.76340.2921360.23422809X-RAY DIFFRACTION98
2.7634-2.93650.24061300.21982763X-RAY DIFFRACTION98
2.9365-3.16320.26211330.22462791X-RAY DIFFRACTION98
3.1632-3.48140.26411310.21692779X-RAY DIFFRACTION97
3.4814-3.98490.25241390.18722731X-RAY DIFFRACTION97
3.9849-5.01930.19891450.16632727X-RAY DIFFRACTION96
5.0193-43.53150.20411570.16962700X-RAY DIFFRACTION96

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