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- PDB-5xi0: Crystal structure of FabV, a new class of enyl-acyl carrier prote... -

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Basic information

Entry
Database: PDB / ID: 5xi0
TitleCrystal structure of FabV, a new class of enyl-acyl carrier protein reductase from Vibrio fischeri
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / enoyl-acyl carrier protein reductase / FabV
Function / homology
Function and homology information


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
Enoyl-[acyl-carrier-protein] reductase [NADH]
Similarity search - Component
Biological speciesVibrio fischeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.087 Å
AuthorsPark, A.K.
CitationJournal: To Be Published
Title: Crystal structure of FabV, a new class of enyl-acyl carrier protein reductase from Vibrio fischeri
Authors: Park, A.K.
History
DepositionApr 25, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]


Theoretical massNumber of molelcules
Total (without water)87,6372
Polymers87,6372
Non-polymers00
Water6,828379
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]


Theoretical massNumber of molelcules
Total (without water)43,8181
Polymers43,8181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Enoyl-[acyl-carrier-protein] reductase [NADH]


Theoretical massNumber of molelcules
Total (without water)43,8181
Polymers43,8181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.998, 109.175, 119.831
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-657-

HOH

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Components

#1: Protein Enoyl-[acyl-carrier-protein] reductase [NADH] / ENR


Mass: 43818.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio fischeri (strain ATCC 700601 / ES114) (bacteria)
Strain: ATCC 700601 / ES114 / Gene: fabV, VF_0888 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5E6G3, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.42 Å3/Da / Density % sol: 49.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1M Bis-tris Propane pH 5.5, 0.1M Sodium Fluoride, 20% (w/v) Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.23986 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23986 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 49667 / % possible obs: 98.6 % / Redundancy: 8.9 % / Biso Wilson estimate: 26.16 Å2 / Rmerge(I) obs: 0.094 / Χ2: 1.516 / Net I/σ(I): 9.2 / Num. measured all: 443849
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.09-2.135.40.36720090.755181.2
2.13-2.1660.34824440.796199.4
2.16-2.216.20.34224650.832199
2.21-2.256.50.31324550.867199.1
2.25-2.36.60.30124880.903199.3
2.3-2.356.90.27724650.925199.3
2.35-2.417.10.27624600.93199.4
2.41-2.487.30.25724580.989199.5
2.48-2.557.60.22925131.042199.5
2.55-2.638.20.20824941.109199.5
2.63-2.738.60.18124581.18199.4
2.73-2.8490.16724951.261199.7
2.84-2.979.50.14325111.391199.8
2.97-3.1210.20.12125061.526199.7
3.12-3.3211.10.10225241.711199.9
3.32-3.5711.60.08825251.912199.8
3.57-3.9312.20.07725382.073199.9
3.93-4.512.40.06825582.298199.9
4.5-5.6712.50.06425852.288199.9
5.67-5012.20.05427162.14199.1

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data collection
SCALEPACKdata scaling
PDB_EXTRACT3.22data extraction
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S8M

3s8m


Resolution: 2.087→40.343 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 27.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2719 2423 4.89 %
Rwork0.2063 47176 -
obs0.2094 49599 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.41 Å2 / Biso mean: 29.9783 Å2 / Biso min: 11.76 Å2
Refinement stepCycle: final / Resolution: 2.087→40.343 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6152 0 0 379 6531
Biso mean---29.7 -
Num. residues----800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086264
X-RAY DIFFRACTIONf_angle_d0.9118486
X-RAY DIFFRACTIONf_chiral_restr0.052956
X-RAY DIFFRACTIONf_plane_restr0.0061100
X-RAY DIFFRACTIONf_dihedral_angle_d7.8293764
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0869-2.12950.34471540.3222623277796
2.1295-2.17580.35391510.3022756290799
2.1758-2.22640.36911380.27662698283699
2.2264-2.28210.32411440.26462751289599
2.2821-2.34380.28311330.24932733286699
2.3438-2.41270.30961480.23762751289999
2.4127-2.49060.30231230.238627622885100
2.4906-2.57960.30151420.22482723286599
2.5796-2.68280.31371390.22752776291599
2.6828-2.80490.27071470.232227682915100
2.8049-2.95270.32241420.241427862928100
2.9527-3.13770.31681400.23627772917100
3.1377-3.37980.28981400.211227842924100
3.3798-3.71970.26271540.195428232977100
3.7197-4.25750.21781410.157528102951100
4.2575-5.3620.20031470.144828623009100
5.362-40.35010.20961400.14842993313399

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