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- PDB-1cwu: BRASSICA NAPUS ENOYL ACP REDUCTASE A138G MUTANT COMPLEXED WITH NA... -

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Basic information

Entry
Database: PDB / ID: 1cwu
TitleBRASSICA NAPUS ENOYL ACP REDUCTASE A138G MUTANT COMPLEXED WITH NAD+ AND THIENODIAZABORINE
ComponentsENOYL ACP REDUCTASE
KeywordsOXIDOREDUCTASE / PLANT LIPID BIOSYNTHESIS / DIAZABORINE
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 / Chem-TDB / Enoyl-[acyl-carrier-protein] reductase [NADH], chloroplastic
Similarity search - Component
Biological speciesBrassica napus (rape)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsRoujeinikova, A. / Rafferty, J.B. / Rice, D.W.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: Inhibitor binding studies on enoyl reductase reveal conformational changes related to substrate recognition.
Authors: Roujeinikova, A. / Sedelnikova, S. / de Boer, G.J. / Stuitje, A.R. / Slabas, A.R. / Rafferty, J.B. / Rice, D.W.
History
DepositionAug 26, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 22, 2014Group: Derived calculations
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6Nov 3, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENOYL ACP REDUCTASE
B: ENOYL ACP REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5186
Polymers62,6472
Non-polymers1,8714
Water2,036113
1
A: ENOYL ACP REDUCTASE
B: ENOYL ACP REDUCTASE
hetero molecules

A: ENOYL ACP REDUCTASE
B: ENOYL ACP REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,03612
Polymers125,2944
Non-polymers3,7428
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_565-x,-y+1,z1
Buried area23540 Å2
ΔGint-168 kcal/mol
Surface area35190 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)104.58, 104.58, 283.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein ENOYL ACP REDUCTASE


Mass: 31323.445 Da / Num. of mol.: 2 / Mutation: A138G
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


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-TDB / 6-METHYL-2(PROPANE-1-SULFONYL)-2H-THIENO[3,2-D][1,2,3]DIAZABORININ-1-OL / Diazaborine


Mass: 272.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13BN2O3S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 3.1 Å3/Da / Density % sol: 60.29 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 4.5 M NACL AND 50 MM NA ACETATE, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 17K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17.5 mg/mlprotein1drop
21.5 mMNAD+1drop
30.75 mMthienodiazaborine1drop
42.25 M1dropNaCl
550 mMsodium acetate1drop
64.5 M1reservoirNaCl
750 mMsodium acetate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.99
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 25755 / % possible obs: 93 % / Rmerge(I) obs: 0.057
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.188 / % possible all: 93.2
Reflection
*PLUS
% possible obs: 93 % / Num. measured all: 90629
Reflection shell
*PLUS
% possible obs: 93 %

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Processing

Software
NameClassification
AMoREphasing
TNTrefinement
XDSdata reduction
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.5→10 Å
Details: THE SIDE CHAINS FOR RESIDUES GLU A 81,GLU A 100,ASP A 101,VAL A 102,LYS A 103, LYS A 106,ARG A 107,LYS A 153,ASN B 57,ARG B 64,ARG B 65,LYS B 67,GLN B 70,GLU B 81,GLU B 96,GLU B 100,ASP B ...Details: THE SIDE CHAINS FOR RESIDUES GLU A 81,GLU A 100,ASP A 101,VAL A 102,LYS A 103, LYS A 106,ARG A 107,LYS A 153,ASN B 57,ARG B 64,ARG B 65,LYS B 67,GLN B 70,GLU B 81,GLU B 96,GLU B 100,ASP B 101,LYS B 103,LYS B 106,ARG B 107,GLN B 125,LYS B 153 HAVE BEEN CURTAILED AT THE BETA CARBON BECAUSE OF POOR ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.314 1305 -RANDOM
Rwork0.211 ---
all-25755 --
obs-24431 93 %-
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4319 0 122 113 4554
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg1.4
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
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 1.4

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