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- PDB-1enp: BRASSICA NAPUS ENOYL ACP REDUCTASE/NADH BINARY COMPLEX AT PH 8.0 ... -

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Basic information

Entry
Database: PDB / ID: 1enp
TitleBRASSICA NAPUS ENOYL ACP REDUCTASE/NADH BINARY COMPLEX AT PH 8.0 AND ROOM TEMPERATURE
ComponentsENOYL ACYL CARRIER PROTEIN REDUCTASE
KeywordsOXIDOREDUCTASE / PLANT LIPID BIOSYNTHESIS
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 / Enoyl-[acyl-carrier-protein] reductase [NADH], chloroplastic
Similarity search - Component
Biological speciesBrassica napus (rape)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsRafferty, J.B. / Rice, D.W.
Citation
Journal: Structure / Year: 1995
Title: Common themes in redox chemistry emerge from the X-ray structure of oilseed rape (Brassica napus) enoyl acyl carrier protein reductase.
Authors: Rafferty, J.B. / Simon, J.W. / Baldock, C. / Artymiuk, P.J. / Baker, P.J. / Stuitje, A.R. / Slabas, A.R. / Rice, D.W.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization of the Nadh-Specific Enoyl Acyl Carrier Protein Reductase from Brassica Napus
Authors: Rafferty, J.B. / Simon, J.W. / Stuitje, A.R. / Slabas, A.R. / Fawcett, T. / Rice, D.W.
History
DepositionOct 18, 1995Processing site: BNL
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: ENOYL ACYL CARRIER PROTEIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6412
Polymers32,9771
Non-polymers6631
Water97354
1
A: ENOYL ACYL CARRIER PROTEIN REDUCTASE
hetero molecules

A: ENOYL ACYL CARRIER PROTEIN REDUCTASE
hetero molecules

A: ENOYL ACYL CARRIER PROTEIN REDUCTASE
hetero molecules

A: ENOYL ACYL CARRIER PROTEIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,5628
Polymers131,9094
Non-polymers2,6544
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 area20800 Å2
ΔGint-137 kcal/mol
Surface area39260 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)70.500, 70.500, 117.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein ENOYL ACYL CARRIER PROTEIN REDUCTASE


Mass: 32977.156 Da / Num. of mol.: 1 / Mutation: S1A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brassica napus (rape) / Tissue: SEED / Gene: PEAR7 CLONE / Organ: SEED / Plasmid: PEAR2 / Gene (production host): PEAR7 CLONE / Production host: Escherichia coli (E. coli)
References: UniProt: P80030, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 41 %
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion, hanging drop / pH: 6.2
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

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Apr 11, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 8364 / % possible obs: 88 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.043
Reflection
*PLUS
Num. measured all: 58714

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Processing

Software
NameClassification
TNTrefinement
SDMSdata reduction
RefinementResolution: 2.6→10 Å / Num. reflection obs: 8364 / σ(F): 0
Details: THE STRUCTURE OF THE BINARY COMPLEX WITH NADH WAS DETERMINED BY DIFFERENCE FOURIER ANALYSIS USING DATA FROM CRYSTALS GROWN WITH NAD WHICH WERE THEN SOAKED IN NADH. THE ELECTRON DENSITY IS ...Details: THE STRUCTURE OF THE BINARY COMPLEX WITH NADH WAS DETERMINED BY DIFFERENCE FOURIER ANALYSIS USING DATA FROM CRYSTALS GROWN WITH NAD WHICH WERE THEN SOAKED IN NADH. THE ELECTRON DENSITY IS CLEARLY INTERPRETABLE FOR THE ENTIRE NADH COFACTOR INCLUDING THE NICOTINAMIDE MOIETY. THE ONLY SIGNIFICANT DIFFERENCE FROM THE STRUCTURE WITH NAD BOUND IS THE MOVEMENT OF THE SIDE CHAIN OF TYR 32 (WHICH WOULD OTHERWISE HAVE OCCUPIED SOME OF THE BINDING POCKET FOR THE NICOTINAMIDE RING) AND SMALL CHANGES ARE NOTED IN THE POSITIONS OF THE MAIN CHAIN FOR RESIDUES GLY 234, PRO 235, LEU 236, AND GLY 237.
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2181 0 44 54 2279
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_bond_d0.0151
X-RAY DIFFRACTIONt_angle_deg1.93
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_planes0.0175
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.132
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27 Å2

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