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- PDB-1d7o: CRYSTAL STRUCTURE OF BRASSICA NAPUS ENOYL ACYL CARRIER PROTEIN RE... -

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Basic information

Entry
Database: PDB / ID: 1d7o
TitleCRYSTAL STRUCTURE OF BRASSICA NAPUS ENOYL ACYL CARRIER PROTEIN REDUCTASE COMPLEXED WITH NAD AND TRICLOSAN
ComponentsENOYL-[ACYL-CARRIER PROTEIN] REDUCTASE (NADH) PRECURSOR
KeywordsOXIDOREDUCTASE / TRICLOSAN / ENOYL REDUCTASE
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / chloroplast / fatty acid biosynthetic process
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / TRICLOSAN / Enoyl-[acyl-carrier-protein] reductase [NADH], chloroplastic
Similarity search - Component
Biological speciesBrassica napus (rape)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsRoujeinikova, A. / Levy, C. / Rowsell, S. / Sedelnikova, S. / Baker, P.J. / Minshull, C.A. / Mistry, A. / Colls, J.G. / Camble, R. / Stuitje, A.R. ...Roujeinikova, A. / Levy, C. / Rowsell, S. / Sedelnikova, S. / Baker, P.J. / Minshull, C.A. / Mistry, A. / Colls, J.G. / Camble, R. / Stuitje, A.R. / Slabas, A.R. / Rafferty, J.B. / Pauptit, R.A. / Viner, R. / Rice, D.W.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Crystallographic analysis of triclosan bound to enoyl reductase.
Authors: Roujeinikova, A. / Levy, C.W. / Rowsell, S. / Sedelnikova, S. / Baker, P.J. / Minshull, C.A. / Mistry, A. / Colls, J.G. / Camble, R. / Stuitje, A.R. / Slabas, A.R. / Rafferty, J.B. / ...Authors: Roujeinikova, A. / Levy, C.W. / Rowsell, S. / Sedelnikova, S. / Baker, P.J. / Minshull, C.A. / Mistry, A. / Colls, J.G. / Camble, R. / Stuitje, A.R. / Slabas, A.R. / Rafferty, J.B. / Pauptit, R.A. / Viner, R. / Rice, D.W.
#1: Journal: Structure / Year: 1995
Title: Common themes in redox chemistry emerge from the X-ray structure of oil seed rape (Brassica napus) enoyl acyl carrier protein reductase
Authors: Rafferty, J.B. / Simon, J.W. / Stuitje, A.R. / Slabas, A.R. / Fawsett, T. / Rice, D.W.
History
DepositionOct 19, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENOYL-[ACYL-CARRIER PROTEIN] REDUCTASE (NADH) PRECURSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3473
Polymers31,3951
Non-polymers9532
Water1,58588
1
A: ENOYL-[ACYL-CARRIER PROTEIN] REDUCTASE (NADH) PRECURSOR
hetero molecules

A: ENOYL-[ACYL-CARRIER PROTEIN] REDUCTASE (NADH) PRECURSOR
hetero molecules

A: ENOYL-[ACYL-CARRIER PROTEIN] REDUCTASE (NADH) PRECURSOR
hetero molecules

A: ENOYL-[ACYL-CARRIER PROTEIN] REDUCTASE (NADH) PRECURSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,39012
Polymers125,5784
Non-polymers3,8128
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_556-y,-x,-z+11
Buried area23950 Å2
ΔGint-232 kcal/mol
Surface area37410 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.5, 70.5, 118.0
Angle α, β, γ (deg.)90, 90, 90
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein ENOYL-[ACYL-CARRIER PROTEIN] REDUCTASE (NADH) PRECURSOR


Mass: 31394.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brassica napus (rape) / Production host: Escherichia coli (E. coli)
References: UniProt: P80030, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-TCL / TRICLOSAN / Triclosan


Mass: 289.542 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H7Cl3O2 / Comment: antifungal, antibiotic, detergent*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal
*PLUS
Density % sol: 41 %
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 6.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlenzyme1drop
210 mM1dropNaPO4
31 mMdithiothreitol1drop
40.15 Mnucleotide1reservoir
52.0 Mammonium sulfate1reservoir
60.1 MHEPES/NaOH1reservoir
7NAD+1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 23195 / % possible obs: 96 % / Rmerge(I) obs: 0.055
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.3 / % possible all: 98
Reflection shell
*PLUS
% possible obs: 98 % / Num. unique obs: 1547

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Processing

Software
NameClassification
TNTrefinement
MAR345data collection
SCALEPACKdata scaling
RefinementResolution: 1.9→10 Å /
RfactorSelection details
Rfree0.225 5% RANDOM
Rwork0.162 -
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2173 0 61 88 2322
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg1.7
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd

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