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- PDB-1dfh: X-RAY STRUCTURE OF ESCHERICHIA COLI ENOYL REDUCTASE WITH BOUND NA... -

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Basic information

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


enoyl-[acyl-carrier-protein] reductase [NAD(P)H] activity / 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 [NAD(P)H] activity / 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 / identical protein binding / membrane / 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 / Chem-TDB / 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 / Resolution: 2.2 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: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / software / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENOYL ACYL CARRIER PROTEIN REDUCTASE
B: ENOYL ACYL CARRIER PROTEIN REDUCTASE
A: 6-METHYL-2(PROPANE-1-SULFONYL)-2H-THIENO[3,2-D][1,2,3]DIAZABORININ-1-OL
B: 6-METHYL-2(PROPANE-1-SULFONYL)-2H-THIENO[3,2-D][1,2,3]DIAZABORININ-1-OL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3956
Polymers55,5232
Non-polymers1,8714
Water00
1
A: ENOYL ACYL CARRIER PROTEIN REDUCTASE
B: ENOYL ACYL CARRIER PROTEIN REDUCTASE
hetero molecules

A: ENOYL ACYL CARRIER PROTEIN REDUCTASE
B: ENOYL ACYL CARRIER PROTEIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,78912
Polymers111,0474
Non-polymers3,7428
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
Buried area21670 Å2
ΔGint-126 kcal/mol
Surface area31160 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.900, 80.900, 328.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.65, 0.605, -0.459), (0.606, 0.049, -0.794), (-0.458, -0.794, -0.399)
Vector: 42.52, 148.48, 228.46001)

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Components

#1: Protein ENOYL ACYL CARRIER PROTEIN REDUCTASE / ENR


Mass: 27761.730 Da / Num. of mol.: 2
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


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

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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: 2.77 Å3/Da / Density % sol: 55.6 %
Crystal growpH: 5
Details: 15% PEG 400, PH5.0 100MM ACETATE, 5MM NAD, 5MM 1,2-DIHYDRO-1-HYDROXY-2-(PROP-1-YLSULPHONYL)(5- METHYLTHIENO)[3,2-E][1,2,3]DIAZABORINE
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
515 %PEG4001reservoir
6100 mMacetate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 26, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.2→20.6 Å / Num. obs: 31179 / % possible obs: 95 % / Redundancy: 2.4 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 8.98
Reflection shellResolution: 2.21→2.26 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.139 / Mean I/σ(I) obs: 5.2 / % possible all: 56.6
Reflection
*PLUS
Num. measured all: 76176

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Processing

Software
NameClassification
CCP4model building
TNTrefinement
MOSFLMdata reduction
Agrovatadata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: E. COLI ENR

Resolution: 2.2→10 Å / Stereochemistry target values: ENGH AND HUBER
Details: INITIALLY THE NAD AND THIENO-DIAZABORINE WERE REFINED INDEPENDENTLY AND NOT RESTRAINED BY THE COVALENT BOND BETWEEN THEM. AFTER TWO CYCLES OF REFINEMENT IT WAS CLEAR THAT THEY WERE BOUND ...Details: INITIALLY THE NAD AND THIENO-DIAZABORINE WERE REFINED INDEPENDENTLY AND NOT RESTRAINED BY THE COVALENT BOND BETWEEN THEM. AFTER TWO CYCLES OF REFINEMENT IT WAS CLEAR THAT THEY WERE BOUND COVALENTLY AND THIS RESTRAINT WAS ADDED. 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
Rwork0.194 --
all-30825 -
obs-30825 93 %
Solvent computationBsol: 182.9 Å2 / ksol: 0.85 e/Å3
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3814 0 122 0 3936
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01240102
X-RAY DIFFRACTIONt_angle_deg1.60854113
X-RAY DIFFRACTIONt_dihedral_angle_d16.08623630
X-RAY DIFFRACTIONt_incorr_chiral_ct2
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.01864
X-RAY DIFFRACTIONt_gen_planes0.0165919
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd0.365260
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.014
X-RAY DIFFRACTIONt_plane_restr0.0169

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