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- PDB-4bkq: Enoyl-ACP reductase from Yersinia pestis (wildtype)with cofactor NADH -

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Basic information

Entry
Database: PDB / ID: 4bkq
TitleEnoyl-ACP reductase from Yersinia pestis (wildtype)with cofactor NADH
ComponentsPUTATIVE REDUCTASE YPZ3_3519
KeywordsOXIDOREDUCTASE / FATTY ACID BIOSYNTHESIS
Function / homology
Function and homology information


trans-2-enoyl-CoA reductase (NADH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD binding / fatty acid biosynthetic process
Similarity search - Function
: / Trans-2-enoyl-CoA reductase / Enoyl reductase FAD binding domain / Trans-2-enoyl-CoA reductase catalytic domain, putative / Enoyl reductase FAD binding domain / Trans-2-enoyl-CoA reductase catalytic region / NAD(P)H binding domain of trans-2-enoyl-CoA reductase / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesYERSINIA PESTIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHirschbeck, M.W. / Neckles, C. / Tonge, P.J. / Kisker, C.
CitationJournal: Biochemistry / Year: 2016
Title: Selectivity of Pyridone- and Diphenyl Ether-Based Inhibitors for the Yersinia Pestis Fabv Enoyl-Acp Reductase.
Authors: Neckles, C. / Pschibul, A. / Lai, C. / Hirschbeck, M. / Kuper, J. / Davoodi, S. / Zou, J. / Liu, N. / Pan, P. / Shah, S. / Daryaee, F. / Bommineni, G.R. / Lai, C. / Simmerling, C. / Kisker, C. / Tonge, P.J.
History
DepositionApr 29, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Jun 15, 2016Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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: PUTATIVE REDUCTASE YPZ3_3519
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6012
Polymers45,9361
Non-polymers6651
Water59433
1
A: PUTATIVE REDUCTASE YPZ3_3519
hetero molecules

A: PUTATIVE REDUCTASE YPZ3_3519
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,2024
Polymers91,8712
Non-polymers1,3312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area5740 Å2
ΔGint-11.3 kcal/mol
Surface area32140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.628, 102.628, 214.913
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein PUTATIVE REDUCTASE YPZ3_3519 / ENOYL-ACP REDUCATSE / TRANS-2-ENOYL-COA REDUCTASE


Mass: 45935.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA PESTIS (bacteria) / Strain: A1122 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8Z9U1, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH


Mass: 665.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H29N7O14P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.81 Å3/Da / Density % sol: 56.24 % / Description: NONE
Crystal growDetails: 1.2-1.5 M SODIUM MALONATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.918
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.3→46.31 Å / Num. obs: 30614 / % possible obs: 100 % / Observed criterion σ(I): 2.6 / Redundancy: 10.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 20.1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7_650)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZU2

3zu2


Resolution: 2.3→45.98 Å / SU ML: 0.33 / σ(F): 0 / Phase error: 26.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2298 1440 5 %
Rwork0.1943 --
obs0.1961 28758 94.14 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.234 Å2 / ksol: 0.347 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.9367 Å20 Å20 Å2
2--9.9367 Å20 Å2
3----19.8735 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3171 0 44 33 3248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073293
X-RAY DIFFRACTIONf_angle_d1.084473
X-RAY DIFFRACTIONf_dihedral_angle_d16.241210
X-RAY DIFFRACTIONf_chiral_restr0.072496
X-RAY DIFFRACTIONf_plane_restr0.004580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.38220.3441160.29722291X-RAY DIFFRACTION81
2.3822-2.47760.34971460.29652412X-RAY DIFFRACTION86
2.4776-2.59030.39851440.30252518X-RAY DIFFRACTION89
2.5903-2.72690.3411270.29082629X-RAY DIFFRACTION92
2.7269-2.89770.33241350.24952731X-RAY DIFFRACTION96
2.8977-3.12140.32271400.25162843X-RAY DIFFRACTION98
3.1214-3.43540.23691390.22242884X-RAY DIFFRACTION99
3.4354-3.93230.22331580.18672907X-RAY DIFFRACTION100
3.9323-4.95330.18081870.14932931X-RAY DIFFRACTION100
4.9533-45.98890.18491480.16083172X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.65550.1679-0.0020.4109-0.26560.5294-0.0538-0.268-0.26570.5005-0.1613-0.0656-0.09150.00550.08270.58570.07230.05190.40120.03430.333721.4727-10.867313.4186
20.0682-0.094-0.05980.30770.2950.47380.00790.0134-0.0963-0.2007-0.07240.17610.02950.18670.05750.46530.06870.05240.3677-0.00450.403321.365-12.9213-9.7281
30.0283-00.04690.00980.00310.1121-0.030.04410.0549-0.2518-0.11040.1154-0.1574-0.00430.06360.50350.0867-0.05660.3266-0.0170.4788.9961-8.393-14.5626
40.0384-0.02130.02010.04380.05140.07180.00270.1283-0.0872-0.0139-0.16480.15370.2141-0.04290.05690.83050.02030.00260.337-0.09630.5875.6558-26.4223-9.9617
50.2711-0.1178-0.18980.12960.00990.2007-0.24690.0979-0.2095-0.1622-0.21360.30.307-0.11430.15580.94720.0598-0.04180.3352-0.09860.59717.3831-28.649-10.508
60.07250.0245-0.040.03380.04820.2014-0.04070.1095-0.221-0.2535-0.08980.22020.31560.1201-0.05811.04910.30640.05970.2165-0.1620.486418.1022-31.8951-13.9877
70.0174-0.02110.00130.0587-0.07910.2047-0.05730.0482-0.0084-0.0002-0.0528-0.021-0.0223-0.04550.03481.13780.15580.26840.896-0.08040.649625.4574-28.1806-28.2543
80.2168-0.117-0.0030.40990.01310.0017-0.05470.0019-0.14580.15340.0521-0.07610.06850.0139-0.01671.140.51410.07470.4081-0.08770.462725.0243-42.1047-7.8742
90.17660.00140.07070.00780.01230.0459-0.0739-0.0120.0554-0.0463-0.0184-0.15640.23650.21610.04570.6610.14420.04010.42430.01160.451826.4074-21.08836.1394
100.0218-0.03340.04620.179-0.20360.2351-0.03940.02110.01030.0053-0.0538-0.0163-0.0670.05260.01150.46470.08280.0140.40830.0580.41712.676-3.7362-5.5026
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 8:50)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 51:123)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 124:150)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 151:190)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 191:243)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 244:340)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 341:347)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 348:382)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 383:414)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 415:422)

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