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- PDB-1dfi: X-RAY STRUCTURE OF ESCHERICHIA COLI ENOYL REDUCTASE WITH BOUND NAD -

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Basic information

Entry
Database: PDB / ID: 1dfi
TitleX-RAY STRUCTURE OF ESCHERICHIA COLI ENOYL REDUCTASE WITH BOUND NAD
ComponentsENOYL ACYL CARRIER PROTEIN REDUCTASE
KeywordsOXIDOREDUCTASE / LIPID BIOSYNTHESIS
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / NADH binding / biotin biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / lipid biosynthetic process / catalytic complex / protein homotetramerization / response to antibiotic ...enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / NADH binding / biotin biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / lipid biosynthetic process / catalytic complex / protein homotetramerization / response to antibiotic / protein-containing complex / membrane / identical protein binding / cytosol
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] FabI / Enoyl-[acyl-carrier-protein] reductase [NADH] FabI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, ISOMORPHOUS REPLACEMENT / Resolution: 2.09 Å
AuthorsBaldock, C. / Rafferty, J.B. / Rice, D.W.
Citation
Journal: Science / Year: 1996
Title: A mechanism of drug action revealed by structural studies of enoyl reductase.
Authors: Baldock, C. / Rafferty, J.B. / Sedelnikova, S.E. / Baker, P.J. / Stuitje, A.R. / Slabas, A.R. / Hawkes, T.R. / Rice, D.W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Crystallization of Escherichia Coli Enoyl Reductase and its Complex with Diazaborine
Authors: Baldock, C. / Rafferty, J.B. / Sedelnikova, S.E. / Bithell, S. / Stuitje, A.R. / Slabas, A.R. / Rice, D.W.
History
DepositionJan 16, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / software / 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 / _software.name / _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
B: ENOYL ACYL CARRIER PROTEIN REDUCTASE
C: ENOYL ACYL CARRIER PROTEIN REDUCTASE
D: ENOYL ACYL CARRIER PROTEIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,7018
Polymers111,0474
Non-polymers2,6544
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19060 Å2
ΔGint-109 kcal/mol
Surface area30540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.000, 81.200, 79.000
Angle α, β, γ (deg.)90.00, 92.90, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.795, 0.159, -0.585), (0.158, -0.986, -0.053), (-0.585, -0.05, -0.809)14.51, -0.98, 44.24
2given(-0.812, 0.025, 0.583), (0.018, -0.997, 0.068), (0.583, 0.066, 0.81)19.05, -1.09, -6.12
3given(-0.984, -0.175, -0.001), (-0.175, 0.984, -0.009), (0.002, -0.008, -1)33.13, 3.1, 38.1

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Components

#1: Protein
ENOYL ACYL CARRIER PROTEIN REDUCTASE / ENR


Mass: 27761.730 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PENVM5 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P29132, UniProt: P0AEK4*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growpH: 5 / Details: 12% PEG 400, PH 5.0 ACETATE, 10MM NAD
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Details: Baldock, C., (1996) Acta Crystallogr.,Sect.D, 52, 1181.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
210 mM1dropNaPO4
31 mMdithiothreitol1drop
410 mMNAD+1drop
512 %PEG4001reservoir
6100 mMacetate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 22, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.08→26.35 Å / Num. obs: 51902 / % possible obs: 93.1 % / Redundancy: 2.2 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 8.2
Reflection shellResolution: 2.08→2.14 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.104 / Mean I/σ(I) obs: 4.6 / % possible all: 71.4
Reflection
*PLUS
Num. measured all: 113658

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Processing

Software
NameClassification
CCP4model building
TNTrefinement
MOSFLMdata reduction
Agrovatadata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, ISOMORPHOUS REPLACEMENT
Starting model: BRASSICA NAPUS ENR (PDB ENTRY 1ENO)

1eno


Resolution: 2.09→10 Å / Stereochemistry target values: ENGH AND HUBER
Details: ASN A 155, ASN A 157, ASN B 155, ASN B 157 ARE THE RESIDUES EITHER SIDE OF THE CATALYTIC TYROSINE AND HAVE DIHEDRAL ANGLES WHICH LIE OUTSIDE THEIR EXPECTED RANGE. THIS IS THOUGHT TO ALLOW ...Details: ASN A 155, ASN A 157, ASN B 155, ASN B 157 ARE THE RESIDUES EITHER SIDE OF THE CATALYTIC TYROSINE AND HAVE DIHEDRAL ANGLES WHICH LIE OUTSIDE THEIR EXPECTED RANGE. THIS IS THOUGHT TO ALLOW THE TYROSINE SIDE-CHAIN TO OCCUPY THE CORRECT POSITION WITH RESPECT TO THE POSITION OF THE NICOTINAMIDE RING.
RfactorNum. reflection% reflection
Rwork0.162 --
all-52346 -
obs-52346 93 %
Solvent computationBsol: 275.1 Å2 / ksol: 0.85 e/Å3
Refinement stepCycle: LAST / Resolution: 2.09→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7336 0 176 327 7839
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01376482
X-RAY DIFFRACTIONt_angle_deg1.503103363
X-RAY DIFFRACTIONt_dihedral_angle_d16.46145040
X-RAY DIFFRACTIONt_incorr_chiral_ct2
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0121684
X-RAY DIFFRACTIONt_gen_planes0.01811289
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.188770
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.162
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.0124
X-RAY DIFFRACTIONt_plane_restr0.0189

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