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- PDB-4fbg: Crystal structure of Treponema denticola trans-2-enoyl-CoA reduct... -

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Basic information

Entry
Database: PDB / ID: 4fbg
TitleCrystal structure of Treponema denticola trans-2-enoyl-CoA reductase in complex with NAD
ComponentsPutative reductase TDE_0597
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 / enoyl-[acyl-carrier-protein] 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Trans-2-enoyl-CoA reductase [NADH]
Similarity search - Component
Biological speciesTreponema denticola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 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
DepositionMay 23, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Nov 8, 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_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative reductase TDE_0597
B: Putative reductase TDE_0597
C: Putative reductase TDE_0597
D: Putative reductase TDE_0597
E: Putative reductase TDE_0597
F: Putative reductase TDE_0597
G: Putative reductase TDE_0597
H: Putative reductase TDE_0597
I: Putative reductase TDE_0597
J: Putative reductase TDE_0597
K: Putative reductase TDE_0597
L: Putative reductase TDE_0597
M: Putative reductase TDE_0597
N: Putative reductase TDE_0597
O: Putative reductase TDE_0597
P: Putative reductase TDE_0597
hetero molecules


Theoretical massNumber of molelcules
Total (without water)728,03024
Polymers722,72316
Non-polymers5,3078
Water00
1
A: Putative reductase TDE_0597
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8342
Polymers45,1701
Non-polymers6631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative reductase TDE_0597


Theoretical massNumber of molelcules
Total (without water)45,1701
Polymers45,1701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative reductase TDE_0597


Theoretical massNumber of molelcules
Total (without water)45,1701
Polymers45,1701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Putative reductase TDE_0597


Theoretical massNumber of molelcules
Total (without water)45,1701
Polymers45,1701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Putative reductase TDE_0597
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8342
Polymers45,1701
Non-polymers6631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Putative reductase TDE_0597


Theoretical massNumber of molelcules
Total (without water)45,1701
Polymers45,1701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Putative reductase TDE_0597
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8342
Polymers45,1701
Non-polymers6631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Putative reductase TDE_0597
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8342
Polymers45,1701
Non-polymers6631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: Putative reductase TDE_0597
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8342
Polymers45,1701
Non-polymers6631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: Putative reductase TDE_0597


Theoretical massNumber of molelcules
Total (without water)45,1701
Polymers45,1701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
K: Putative reductase TDE_0597
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8342
Polymers45,1701
Non-polymers6631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
L: Putative reductase TDE_0597


Theoretical massNumber of molelcules
Total (without water)45,1701
Polymers45,1701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
13
M: Putative reductase TDE_0597
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8342
Polymers45,1701
Non-polymers6631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
14
N: Putative reductase TDE_0597


Theoretical massNumber of molelcules
Total (without water)45,1701
Polymers45,1701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
15
O: Putative reductase TDE_0597


Theoretical massNumber of molelcules
Total (without water)45,1701
Polymers45,1701
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
16
P: Putative reductase TDE_0597
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8342
Polymers45,1701
Non-polymers6631
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.794, 120.032, 171.288
Angle α, β, γ (deg.)90.800, 104.960, 112.750
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Putative reductase TDE_0597 / trans-2-enoyl-CoA reductase


Mass: 45170.168 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema denticola (bacteria) / Strain: ATCC 35405 / CIP 103919 / DSM 14222 / Gene: TDE_0597 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus
References: UniProt: Q73Q47, trans-2-enoyl-CoA reductase (NAD+)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM

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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: 2.53 Å3/Da / Density % sol: 51.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Bis-Tris, 22% PEG 3350, 10uM sacrosine, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Sep 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 132147 / % possible obs: 95.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.144 / Net I/σ(I): 13.7
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 2.4 / % possible all: 95.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EUF

4euf


Resolution: 3.02→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.878 / Occupancy max: 1 / Occupancy min: 0.8 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.574 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2916 6623 5 %RANDOM
Rwork0.2355 ---
obs0.2383 132077 94.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 175.8 Å2 / Biso mean: 67.8529 Å2 / Biso min: 35.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å2-0.3 Å20.26 Å2
2--2.37 Å2-0.69 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 3.02→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms49438 0 352 0 49790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0250706
X-RAY DIFFRACTIONr_angle_refined_deg1.0651.98368490
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.12956356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.49324.6822234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.599158772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.26915288
X-RAY DIFFRACTIONr_chiral_restr0.0750.27606
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02137888
LS refinement shellResolution: 3.019→3.097 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 442 -
Rwork0.333 8386 -
all-8828 -
obs--86.23 %

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