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- PDB-4ggo: Crystal Structure of Trans-2-Enoyl-CoA Reductase from Treponema d... -

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Basic information

Entry
Database: PDB / ID: 4ggo
TitleCrystal Structure of Trans-2-Enoyl-CoA Reductase from Treponema denticola
ComponentsTrans-2-enoyl-CoA reductase
KeywordsOXIDOREDUCTASE / Rossmann Fold / Reductase
Function / homology
Function and homology information


trans-2-enoyl-CoA reductase (NAD+) / trans-2-enoyl-CoA reductase (NADH) activity / 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
Trans-2-enoyl-CoA reductase [NADH]
Similarity search - Component
Biological speciesTreponema denticola ATCC 35405 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBond-Watts, B.B. / Weeks, A.M. / Chang, M.C.Y.
CitationJournal: Biochemistry / Year: 2012
Title: Biochemical and Structural Characterization of the trans-Enoyl-CoA Reductase from Treponema denticola.
Authors: Bond-Watts, B.B. / Weeks, A.M. / Chang, M.C.
History
DepositionAug 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trans-2-enoyl-CoA reductase
B: Trans-2-enoyl-CoA reductase
C: Trans-2-enoyl-CoA reductase
D: Trans-2-enoyl-CoA reductase


Theoretical massNumber of molelcules
Total (without water)176,4164
Polymers176,4164
Non-polymers00
Water11,548641
1
A: Trans-2-enoyl-CoA reductase


Theoretical massNumber of molelcules
Total (without water)44,1041
Polymers44,1041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Trans-2-enoyl-CoA reductase


Theoretical massNumber of molelcules
Total (without water)44,1041
Polymers44,1041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Trans-2-enoyl-CoA reductase


Theoretical massNumber of molelcules
Total (without water)44,1041
Polymers44,1041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Trans-2-enoyl-CoA reductase


Theoretical massNumber of molelcules
Total (without water)44,1041
Polymers44,1041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.050, 87.050, 91.460
Angle α, β, γ (deg.)106.14, 109.72, 98.52
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Trans-2-enoyl-CoA reductase


Mass: 44103.949 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema denticola ATCC 35405 (bacteria)
Strain: ATCC 35405 / Gene: Codon optimized trans-2-enoyl-CoA reductase, TDE_0597 / Plasmid: pET23a-His10-Tev / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q73Q47, geissoschizine dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 641 / 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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 291 K / pH: 7.5
Details: 0.1 M sodium citrate, pH 7.5, 25% PEG 6000, 2.5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 13, 2011
RadiationMonochromator: DOUBLE FLAT CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 105852 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Biso Wilson estimate: 37.7 Å2 / Rmerge(I) obs: 0.135 / Net I/σ(I): 15.61
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.699 / Mean I/σ(I) obs: 2.6 / % possible all: 88.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXAutoSolmodel building
PHASERphasing
PHENIXAutoRefinerefinement
XDSdata reduction
XSCALEdata scaling
PHENIXAUTOSOLphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GGP

4ggp


Resolution: 2→19.68 Å / SU ML: 0.25 / σ(F): 1.99 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.2347 5291 5 %
Rwork0.2062 --
obs0.2077 105818 94.01 %
all-222904 -
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.6877 Å2
Refinement stepCycle: LAST / Resolution: 2→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12316 0 0 641 12957
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312536
X-RAY DIFFRACTIONf_angle_d0.66116916
X-RAY DIFFRACTIONf_dihedral_angle_d12.6354696
X-RAY DIFFRACTIONf_chiral_restr0.0471872
X-RAY DIFFRACTIONf_plane_restr0.0032196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.38021480.32312819X-RAY DIFFRACTION79
2.0227-2.04640.35781690.30583207X-RAY DIFFRACTION91
2.0464-2.07140.31931800.2913420X-RAY DIFFRACTION94
2.0714-2.09750.30251720.26253267X-RAY DIFFRACTION94
2.0975-2.12510.30751820.26563443X-RAY DIFFRACTION94
2.1251-2.15420.31441760.26443345X-RAY DIFFRACTION94
2.1542-2.18490.33261770.25523371X-RAY DIFFRACTION94
2.1849-2.21750.28341780.25983392X-RAY DIFFRACTION94
2.2175-2.25210.28421720.25093273X-RAY DIFFRACTION95
2.2521-2.2890.29811810.23823440X-RAY DIFFRACTION95
2.289-2.32840.29081760.23433345X-RAY DIFFRACTION95
2.3284-2.37070.26421770.23623362X-RAY DIFFRACTION94
2.3707-2.41620.29871800.2253414X-RAY DIFFRACTION95
2.4162-2.46540.28521780.22393383X-RAY DIFFRACTION95
2.4654-2.51890.26241770.22433348X-RAY DIFFRACTION95
2.5189-2.57740.26041800.22183420X-RAY DIFFRACTION95
2.5774-2.64170.27321780.21743383X-RAY DIFFRACTION95
2.6417-2.71290.23611790.21593403X-RAY DIFFRACTION96
2.7129-2.79250.26821770.21483377X-RAY DIFFRACTION95
2.7925-2.88240.26171790.20773404X-RAY DIFFRACTION95
2.8824-2.98510.24311790.20813403X-RAY DIFFRACTION95
2.9851-3.10420.24161800.21533418X-RAY DIFFRACTION95
3.1042-3.24490.22191780.21833388X-RAY DIFFRACTION95
3.2449-3.41510.24771780.21083367X-RAY DIFFRACTION95
3.4151-3.62780.23481750.20173335X-RAY DIFFRACTION94
3.6278-3.90590.22171750.18193327X-RAY DIFFRACTION94
3.9059-4.29530.19511760.17173329X-RAY DIFFRACTION93
4.2953-4.90840.17931740.16543312X-RAY DIFFRACTION93
4.9084-6.15250.20651780.19953387X-RAY DIFFRACTION95
6.1525-19.68130.15391820.16483445X-RAY DIFFRACTION97

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