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- PDB-6q1y: Crystal Structure of Enoyl-[acyl-carrier-protein] reductase from ... -

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Basic information

Entry
Database: PDB / ID: 6q1y
TitleCrystal Structure of Enoyl-[acyl-carrier-protein] reductase from Mycobacterium avium with bound NAD
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / SSGCID / Enoyl-[acyl-carrier-protein] reductase / NAD / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / trans-2-enoyl-CoA reductase (NADH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesMycobacterium avium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Enoyl-[acyl-carrier-protein] reductase from Mycobacterium avium with bound NAD
Authors: Romanaggi, C.T. / Mayclin, S.J. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionAug 6, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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 [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0347
Polymers29,7551
Non-polymers1,2796
Water6,179343
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.320, 95.320, 139.590
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-306-

PG4

21A-488-

HOH

31A-532-

HOH

41A-697-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Enoyl-[acyl-carrier-protein] reductase [NADH] / MyavA.00170.a.B1


Mass: 29755.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium (strain 104) (bacteria)
Strain: 104 / Gene: MAV_3294 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0H2ZSV5, enoyl-[acyl-carrier-protein] reductase (NADH)

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Non-polymers , 6 types, 349 molecules

#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.08 Å3/Da / Density % sol: 60.02 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MyavA.00170.a.B1.PS38585 @ 20.93 mg/mL, incubated with 5 mM NAD, mixed 0.4uL protein ligand complex + 0.4uL JCSG+ (D10): 40% (v/v) PEG300, 100 mM Sodium Cacodylate/ HCl pH 6.5, 200 mM ...Details: MyavA.00170.a.B1.PS38585 @ 20.93 mg/mL, incubated with 5 mM NAD, mixed 0.4uL protein ligand complex + 0.4uL JCSG+ (D10): 40% (v/v) PEG300, 100 mM Sodium Cacodylate/ HCl pH 6.5, 200 mM Calcium acetate. Tray ID: 310540 D10, puck: ixz5-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 11, 2019 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.65→41.275 Å / Num. obs: 45632 / % possible obs: 99.8 % / Redundancy: 17.614 % / Biso Wilson estimate: 27.223 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.058 / Χ2: 1.07 / Net I/σ(I): 32.41 / Num. measured all: 803764
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.65-1.6914.8920.5514.9949278330933090.9820.57100
1.69-1.7417.6430.456.8257199324232420.9830.464100
1.74-1.7918.2060.368.5557277314631460.9910.37100
1.79-1.8418.1840.27511.2555516305330530.9920.283100
1.84-1.9118.2530.20914.5154212297029700.9960.215100
1.91-1.9718.2040.16318.4252101286228620.9970.167100
1.97-2.0518.2170.1322.9350534277427740.9980.133100
2.05-2.1318.180.10727.8548831268626860.9980.11100
2.13-2.2218.1090.08633.6347048259825980.9990.089100
2.22-2.3318.1030.07637.7844569246324620.9990.078100
2.33-2.4618.0090.06643.3542537236123620.9990.068100
2.46-2.6117.9820.06146.3840047222922270.9990.06399.9
2.61-2.7917.8070.05451.9737698212021170.9990.05699.9
2.79-3.0117.6280.04856.4334762197619720.9990.04999.8
3.01-3.317.4080.04363.2131683182718200.9990.04499.6
3.3-3.6916.9530.03867.05282601677166710.03999.4
3.69-4.2616.8720.03471.26248181481147110.03599.3
4.26-5.2216.8080.03172.5213961285127310.03299.1
5.22-7.3816.7250.02970.43170601037102010.0398.4
7.38-41.27514.8720.02669.1389386326010.9990.02795.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(dev_3584: ???)refinement
PDB_EXTRACT3.25data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H7I

2h7i
PDB Unreleased entry


Resolution: 1.65→41.275 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.68
RfactorNum. reflection% reflectionSelection details
Rfree0.1689 2009 4.41 %random, 0
Rwork0.1416 ---
obs0.1427 45601 99.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.3 Å2 / Biso mean: 24.4317 Å2 / Biso min: 12.04 Å2
Refinement stepCycle: final / Resolution: 1.65→41.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1992 0 85 348 2425
Biso mean--34.42 38.9 -
Num. residues----267
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6501-1.69130.20451330.16823054100
1.6913-1.73710.2141300.16263079100
1.7371-1.78820.17651560.1583034100
1.7882-1.84590.17841480.14873066100
1.8459-1.91190.18951530.14143055100
1.9119-1.98840.16671520.14983070100
1.9884-2.07890.17611580.14613063100
2.0789-2.18850.1711170.1353098100
2.1885-2.32560.17571330.14033133100
2.3256-2.50520.17031530.13983098100
2.5052-2.75720.17441450.14373109100
2.7572-3.15610.1641390.14393165100
3.1561-3.97580.15521460.13153203100
3.9758-41.2750.16181460.14336599
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)
11.25390.36420.43361.77620.27421.214-0.03740.06130.02610.01350.0094-0.2029-0.01090.29420.01590.10380.0087-0.00230.26910.04740.17629.299-37.2635-17.2295
27.2418-3.9796-5.15752.55523.8438.03580.08360.32910.4218-0.2278-0.0606-0.4789-0.33810.3939-0.02430.148-0.089-0.01030.35310.11130.256810.7012-27.8968-29.6383
31.4505-0.3819-0.07460.83920.13760.8665-0.0531-0.03040.11450.0112-0.0078-0.099-0.07110.13450.04080.1265-0.0131-0.0270.17740.03540.1572-5.9468-30.2829-20.9562
40.9547-0.1583-0.08060.65160.18110.78830.010.0010.1129-0.0313-0.0363-0.0205-0.07040.06290.01490.12590.0004-0.00310.16390.02750.1718-8.9315-34.0765-19.548
53.28633.89583.74776.34217.15719.13120.0318-0.19490.08190.1204-0.24520.0562-0.0988-0.06870.20430.10030.0092-0.00720.21910.01840.1435-16.0511-36.6441-1.2449
61.7718-0.2605-0.82051.00610.2642.4945-0.0519-0.1034-0.00260.10590.0008-0.03530.03840.13730.05080.11440.026-0.00430.12120.01990.1327-8.507-47.1411-16.4318
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 67 )A3 - 67
2X-RAY DIFFRACTION2chain 'A' and (resid 68 through 82 )A68 - 82
3X-RAY DIFFRACTION3chain 'A' and (resid 83 through 158 )A83 - 158
4X-RAY DIFFRACTION4chain 'A' and (resid 159 through 208 )A159 - 208
5X-RAY DIFFRACTION5chain 'A' and (resid 209 through 225 )A209 - 225
6X-RAY DIFFRACTION6chain 'A' and (resid 226 through 269 )A226 - 269

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