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- PDB-4eue: Crystal structure of Clostridium acetobutulicum trans-2-enoyl-CoA... -

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Basic information

Entry
Database: PDB / ID: 4eue
TitleCrystal structure of Clostridium acetobutulicum trans-2-enoyl-CoA reductase in complex with NADH
ComponentsPutative reductase CA_C0462
KeywordsOXIDOREDUCTASE / TER / biofuel / synthetic biology / reductase / catalytic mechanism / substrate specificity
Function / homology
Function and homology information


trans-2-enoyl-CoA reductase (NAD+) / trans-2-enoyl-CoA reductase (NADH) activity / fatty acid biosynthetic process / NAD binding
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 / NAD(P)-binding domain superfamily / Rossmann fold ...: / 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 / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Trans-2-enoyl-CoA reductase [NADH]
Similarity search - Component
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsHu, K. / Zhao, M. / Zhang, T. / Yang, S. / Ding, J.
CitationJournal: Biochem.J. / Year: 2013
Title: Structures of trans-2-enoyl-CoA reductases from Clostridium acetobutylicum and Treponema denticola: insights into the substrate specificity and the catalytic mechanism
Authors: Hu, K. / Zhao, M. / Zhang, T. / Zha, M. / Zhong, C. / Jiang, Y. / Ding, J.
History
DepositionApr 25, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative reductase CA_C0462
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9553
Polymers48,2671
Non-polymers6882
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.205, 45.950, 85.431
Angle α, β, γ (deg.)90.000, 90.740, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative reductase CA_C0462 / trans-2-enoyl-CoA reductase


Mass: 48266.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum (bacteria)
Strain: ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787
Gene: CA_C0462 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus
References: UniProt: Q97LU2, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor
#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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 200mM magnesium acetate tetrahydrate, 20% PEG 3350, pH 7.0, temperature 289K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 25, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 29209 / % possible obs: 99.4 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.123
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.459 / % possible all: 99

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0.49 / SU B: 8.206 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 1456 5 %RANDOM
Rwork0.1982 ---
obs0.1997 29116 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 93.67 Å2 / Biso mean: 24.697 Å2 / Biso min: 11.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20.1 Å2
2---0.09 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3217 0 45 230 3492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223326
X-RAY DIFFRACTIONr_angle_refined_deg1.0141.9864474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2875397
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.53224.026154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06715629
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.251522
X-RAY DIFFRACTIONr_chiral_restr0.0740.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212462
X-RAY DIFFRACTIONr_mcbond_it0.5351.51970
X-RAY DIFFRACTIONr_mcangle_it1.11923178
X-RAY DIFFRACTIONr_scbond_it2.23231356
X-RAY DIFFRACTIONr_scangle_it3.7044.51296
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 96 -
Rwork0.234 1987 -
all-2083 -
obs--97.66 %
Refinement TLS params.Method: refined / Origin x: 39.5367 Å / Origin y: 22.0083 Å / Origin z: 23.3668 Å
111213212223313233
T0.0073 Å20.0002 Å20.0027 Å2-0.0049 Å20.001 Å2--0.0046 Å2
L0.1573 °2-0.0304 °20.0301 °2-0.1397 °2-0.0639 °2--0.1704 °2
S0.0088 Å °0.0114 Å °0.0199 Å °-0.0118 Å °-0.0189 Å °-0.0012 Å °0.0204 Å °-0.006 Å °0.0102 Å °

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