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- PDB-6vly: Crystal structure of FabI-NADH complex from Alistipes finegoldii -

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Basic information

Entry
Database: PDB / ID: 6vly
TitleCrystal structure of FabI-NADH complex from Alistipes finegoldii
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADH]
KeywordsOXIDOREDUCTASE / Enoyl-ACP Reductase / FabI
Function / homologyenoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / Enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / NAD(P)-binding domain superfamily / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / Enoyl-[acyl-carrier-protein] reductase [NADH]
Function and homology information
Biological speciesAlistipes finegoldii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsRadka, C.D. / Seetharaman, J. / Rock, C.O.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM034496 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA21765 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: The genome of a Bacteroidetes inhabitant of the human gut encodes a structurally distinct enoyl-acyl carrier protein reductase (FabI).
Authors: Radka, C.D. / Frank, M.W. / Yao, J. / Seetharaman, J. / Miller, D.J. / Rock, C.O.
History
DepositionJan 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 10, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 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]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
C: Enoyl-[acyl-carrier-protein] reductase [NADH]
D: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,96017
Polymers136,5274
Non-polymers3,43413
Water18,8261045
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, elutes as a tetramer, equilibrium centrifugation, sediments as a tetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27660 Å2
ΔGint-162 kcal/mol
Surface area33340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.313, 111.537, 150.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 34131.625 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alistipes finegoldii (bacteria) / Gene: fabI, ERS852447_01935 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A174E195, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH / Nicotinamide adenine dinucleotide


Mass: 665.441 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H29N7O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1045 / Source method: isolated from a natural source / Formula: H2O
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: 2.32 Å3/Da / Density % sol: 46.88 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: Crystallization: 12.5% PEG 1000, 200 mM NaCl, 100 mM MES pH 6.0, Cryo: 12.5% PEG 1000, 200 mM NaCl, 100 mM MES pH 6.0, 25% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 26, 2019
RadiationMonochromator: Double Crystal Monochromator; Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 1.86→29.09 Å / Num. obs: 512333 / % possible obs: 98.7 % / Redundancy: 4.9 % / CC1/2: 0.997 / Net I/σ(I): 12.6
Reflection shellResolution: 1.86→1.91 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 34973 / CC1/2: 0.77 / % possible all: 94.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VLX

6vlx


Resolution: 1.86→29.09 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.921 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1973 5169 4.9 %RANDOM
Rwork0.1583 ---
obs0.1602 100112 98.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 193.12 Å2 / Biso mean: 23.559 Å2 / Biso min: 2.98 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2--0.01 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.86→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8862 0 225 1045 10132
Biso mean--25.58 36.95 -
Num. residues----1144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0139252
X-RAY DIFFRACTIONr_bond_other_d0.0020.0178487
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.6712492
X-RAY DIFFRACTIONr_angle_other_deg1.361.59519662
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.09251140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.43422.323465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91151584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5351557
X-RAY DIFFRACTIONr_chiral_restr0.0720.21215
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210297
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021978
LS refinement shellResolution: 1.86→1.908 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.443 373 -
Rwork0.429 6975 -
obs--93.87 %

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