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- PDB-5msp: Structure of the unmodified PCP-R didomain of carboxylic acid red... -

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Basic information

Entry
Database: PDB / ID: 5msp
TitleStructure of the unmodified PCP-R didomain of carboxylic acid reductase (CAR) from Segniliparus rugosus in complex with NADP, F2221 form
ComponentsThioester reductase domain-containing protein
KeywordsOXIDOREDUCTASE / adenylation domain / carboxylic acid reductase
Function / homology
Function and homology information


long-chain fatty acid-CoA ligase activity / 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 / 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 / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Carboxylic acid reductase
Similarity search - Component
Biological speciesSegniliparus rugosus ATCC BAA-974 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 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
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: Thioester reductase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,1122
Polymers128,3681
Non-polymers7431
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-0 kcal/mol
Surface area20790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.370, 137.680, 202.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222

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Components

#1: Protein Thioester reductase domain-containing protein


Mass: 128368.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Segniliparus rugosus ATCC BAA-974 (bacteria)
Gene: HMPREF9336_01297 / Production host: Escherichia coli (E. coli) / References: UniProt: E5XP76
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: CARsr PCP-Red crystals were obtained in 0.1 M sodium malonate dibasic monohydrate, 0.1 M HEPES pH 7.0, 0.5% Jeffamine ED-2003.

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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: Jul 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.41→101.04 Å / Num. obs: 36214 / % possible obs: 99 % / Redundancy: 5.4 % / CC1/2: 1 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8
Reflection shellResolution: 2.41→2.5 Å / CC1/2: 0.6 / % possible all: 99.5

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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: 2.41→101.04 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 8.887 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.204 / ESU R Free: 0.19 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22697 1728 4.8 %RANDOM
Rwork0.17894 ---
obs0.18117 34488 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 66.76 Å2
Baniso -1Baniso -2Baniso -3
1-6.26 Å20 Å20 Å2
2---1.95 Å20 Å2
3----4.32 Å2
Refinement stepCycle: 1 / Resolution: 2.41→101.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3911 0 40 36 3987
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0194050
X-RAY DIFFRACTIONr_bond_other_d0.0020.023838
X-RAY DIFFRACTIONr_angle_refined_deg1.9121.9715520
X-RAY DIFFRACTIONr_angle_other_deg1.11638816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5555512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68523.799179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.77415626
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7611527
X-RAY DIFFRACTIONr_chiral_restr0.1180.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214601
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02917
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_it5.3466.3142054
X-RAY DIFFRACTIONr_mcbond_other5.3466.3132053
X-RAY DIFFRACTIONr_mcangle_it7.489.4822564
X-RAY DIFFRACTIONr_mcangle_other7.4799.4832565
X-RAY DIFFRACTIONr_scbond_it6.596.9791995
X-RAY DIFFRACTIONr_scbond_other6.5916.981994
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.01510.1582955
X-RAY DIFFRACTIONr_long_range_B_refined12.01850.094375
X-RAY DIFFRACTIONr_long_range_B_other12.01650.0914376
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.41→2.473 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.444 122 -
Rwork0.357 2520 -
obs--99.14 %

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