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

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Basic information

Entry
Database: PDB / ID: 5msu
TitleStructure of the R domain of carboxylic acid reductase (CAR) from Mycobacterium marinum in complex with NADP, P21 form
ComponentsCarboxylic acid reductase
KeywordsOXIDOREDUCTASE / adenylation domain / carboxylic acid reductase
Function / homology
Function and homology information


Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / phosphopantetheine binding / fatty acid metabolic process / NADP binding / ATP binding
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. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase ...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. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Carboxylic acid reductase
Similarity search - Component
Biological speciesMycobacterium marinum M (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsGahloth, D. / 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 5, 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 1.4Jan 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Carboxylic acid reductase
A: Carboxylic acid reductase
B: Carboxylic acid reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)386,0096
Polymers383,7793
Non-polymers2,2303
Water19,8891104
1
C: Carboxylic acid reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,6702
Polymers127,9261
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Carboxylic acid reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,6702
Polymers127,9261
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Carboxylic acid reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,6702
Polymers127,9261
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.540, 58.950, 135.560
Angle α, β, γ (deg.)90.00, 105.92, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11C
21A
12C
22B
13A
23B

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11CA732 - 1174732 - 1174
21AB732 - 1174732 - 1174
12CA732 - 1173732 - 1173
22BC732 - 1173732 - 1173
13AB732 - 1173732 - 1173
23BC732 - 1173732 - 1173

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Carboxylic acid reductase / CAR / ATP/NADPH-dependent carboxylic acid reductase / Fatty acid reductase


Mass: 127926.203 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum M (bacteria) / Gene: car, fadD9, MMAR_2117 / Production host: Escherichia coli (E. coli)
References: UniProt: B2HN69, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1104 / 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: 291 K / Method: vapor diffusion, sitting drop
Details: Co-crystals of CARmm Red domain with NADPH were obtained in 0.2 M ammonium tartrate dibasic, 20% PEG3350 (SG P21)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.74→130.36 Å / Num. obs: 156520 / % possible obs: 100 % / Redundancy: 3.7 % / CC1/2: 1 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.7
Reflection shellResolution: 1.74→1.8 Å / CC1/2: 0.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MSO

5mso


Resolution: 1.74→130.36 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.685 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.105 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21299 7843 5 %RANDOM
Rwork0.1884 ---
obs0.18964 148677 99.71 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 41.321 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20.08 Å2
2--1.37 Å20 Å2
3----0.36 Å2
Refinement stepCycle: 1 / Resolution: 1.74→130.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10252 0 135 1104 11491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01910620
X-RAY DIFFRACTIONr_bond_other_d0.0060.0210022
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.98314495
X-RAY DIFFRACTIONr_angle_other_deg1.269322986
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.77951322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.71523.354480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.93151643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1291590
X-RAY DIFFRACTIONr_chiral_restr0.0750.21644
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112027
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022422
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6742.6215309
X-RAY DIFFRACTIONr_mcbond_other2.6622.6215308
X-RAY DIFFRACTIONr_mcangle_it3.5723.9166624
X-RAY DIFFRACTIONr_mcangle_other3.5723.9166625
X-RAY DIFFRACTIONr_scbond_it3.9833.0225311
X-RAY DIFFRACTIONr_scbond_other3.9823.0225311
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0044.3747872
X-RAY DIFFRACTIONr_long_range_B_refined7.64122.46512853
X-RAY DIFFRACTIONr_long_range_B_other7.6422.46512853
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11C540740.07
12A540740.07
21C523100.09
22B523100.09
31A532460.08
32B532460.08
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 561 -
Rwork0.317 10884 -
obs--99.68 %
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)
11.44230.30150.05020.7784-0.33250.90570.0041-0.14960.00930.042-0.082-0.0186-0.01180.10570.07780.00530.00490.00610.14020.01380.0234-22.201-0.405139.672
22.7207-0.1887-0.38040.3761-0.00691.13190.04660.00680.31380.02590.0095-0.0178-0.03340.0368-0.05610.01660.0186-0.00250.1166-0.0140.08343.268-7.938165.82
30.8557-0.05220.26781.0071-0.15650.58880.06830.152-0.076-0.1559-0.0983-0.04020.09530.04920.030.05570.04080.02590.14370.0060.032-56.531-32.387178.432
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C732 - 1174
2X-RAY DIFFRACTION2A732 - 1174
3X-RAY DIFFRACTION3B713 - 1174

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