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- PDB-2qio: X-Ray Structure of Enoyl-Acyl Carrier Protein Reductase from Baci... -

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Basic information

Entry
Database: PDB / ID: 2qio
TitleX-Ray Structure of Enoyl-Acyl Carrier Protein Reductase from Bacillus Anthracis with Triclosan
ComponentsEnoyl-(Acyl-carrier-protein) reductase
KeywordsUNKNOWN FUNCTION / Enoyl ACP Reductase
Function / homology
Function and homology information


: / enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / nucleotide binding
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / 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] / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsKlein, G.M. / Santarsiero, B.D. / Mesecar, A.D.
CitationJournal: Chemmedchem / Year: 2008
Title: Design and synthesis of aryl ether inhibitors of the Bacillus anthracis enoyl-ACP reductase.
Authors: Tipparaju, S.K. / Mulhearn, D.C. / Klein, G.M. / Chen, Y. / Tapadar, S. / Bishop, M.H. / Yang, S. / Chen, J. / Ghassemi, M. / Santarsiero, B.D. / Cook, J.L. / Johlfs, M. / Mesecar, A.D. / ...Authors: Tipparaju, S.K. / Mulhearn, D.C. / Klein, G.M. / Chen, Y. / Tapadar, S. / Bishop, M.H. / Yang, S. / Chen, J. / Ghassemi, M. / Santarsiero, B.D. / Cook, J.L. / Johlfs, M. / Mesecar, A.D. / Johnson, M.E. / Kozikowski, A.P.
History
DepositionJul 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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)114,90212
Polymers111,0904
Non-polymers3,8128
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21780 Å2
ΔGint-176 kcal/mol
Surface area33700 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.367, 89.024, 186.049
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a tetramer; all four chains are included in the asymmetric unit.

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Components

#1: Protein
Enoyl-(Acyl-carrier-protein) reductase


Mass: 27772.426 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: delta-delta-ANR / Gene: fabI / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81JF8, UniProt: A0A6L8PBX8*PLUS
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


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


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


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.7 Å3/Da / Density % sol: 54.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10 mG/mL protein, 20mM TrisHCL, 150mM NaCl, 10% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.44→20 Å / Num. all: 44930 / Num. obs: 44865 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 40.8 Å2 / Rmerge(I) obs: 0.098 / Χ2: 1.689 / Net I/σ(I): 9.4
Reflection shellResolution: 2.44→2.53 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.223 / Num. unique all: 4329 / Χ2: 0.981 / % possible all: 96.1

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å19.88 Å
Translation2.5 Å19.88 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1C14

1c14


Resolution: 2.44→20 Å / FOM work R set: 0.864 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 2226 4.9 %random
Rwork0.176 ---
obs-44376 97.6 %-
Solvent computationBsol: 27.067 Å2
Displacement parametersBiso mean: 28.748 Å2
Baniso -1Baniso -2Baniso -3
1--0.008 Å20 Å20 Å2
2---2.262 Å20 Å2
3---2.271 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.44→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7800 0 244 416 8460
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_d1.476
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.9
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 44

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.44-2.460.22460.198896942
2.46-2.480.264460.211943989
2.48-2.50.286610.206924985
2.5-2.520.193530.17929982
2.52-2.540.308570.229751032
2.54-2.560.298450.2019621007
2.56-2.580.237390.207948987
2.58-2.610.282570.2079691026
2.61-2.630.266520.1959521004
2.63-2.660.23470.29821029
2.66-2.690.259530.184930983
2.69-2.710.304420.199851027
2.71-2.740.251470.1719751022
2.74-2.770.251460.2089561002
2.77-2.80.214350.179671002
2.8-2.840.195450.1749631008
2.84-2.870.258500.19210021052
2.87-2.910.263570.185910967
2.91-2.940.192500.1799741024
2.94-2.980.258500.1799641014
2.98-3.030.238610.186934995
3.03-3.070.209510.1819701021
3.07-3.120.196420.1769611003
3.12-3.170.258530.1919571010
3.17-3.230.291430.1919571000
3.23-3.280.217590.1869621021
3.28-3.350.194560.167931987
3.35-3.410.224540.1779761030
3.41-3.490.233740.189922996
3.49-3.570.234510.1899771028
3.57-3.660.189580.167927985
3.66-3.760.212580.1719611019
3.76-3.870.209520.1639511003
3.87-3.990.244480.1639741022
3.99-4.130.194420.1549601002
4.13-4.30.168470.1449541001
4.3-4.490.2410.1519731014
4.49-4.720.215500.1589561006
4.72-5.010.21600.1629541014
5.01-5.390.193500.179531003
5.39-5.920.239520.1969751027
5.92-6.750.252480.2259711019
6.75-8.40.203430.1539841027
8.4-200.187550.1510041059
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4nad.param
X-RAY DIFFRACTION5tcl.param

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