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- PDB-6vlx: Crystal structure of FabI from Alistipes finegoldii -

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Basic information

Entry
Database: PDB / ID: 6vlx
TitleCrystal structure of FabI 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 / Enoyl-[acyl-carrier-protein] reductase [NADH]
Function and homology information
Biological speciesAlistipes finegoldii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)68,3553
Polymers68,2632
Non-polymers921
Water7,188399
1
A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules

A: Enoyl-[acyl-carrier-protein] reductase [NADH]
B: Enoyl-[acyl-carrier-protein] reductase [NADH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,7116
Polymers136,5274
Non-polymers1842
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area18490 Å2
ΔGint-116 kcal/mol
Surface area34240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.557, 77.772, 127.561
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-688-

HOH

21B-440-

HOH

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Components

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


Mass: 34131.625 Da / Num. of mol.: 2
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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.2 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: Crystallization: 1.2 M Na K Tartrate, 100 mM Tris pH 8.0, Cryo: 1.3M Na K Tartrate, 100 mM Tris pH 8.0, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 12, 2018
Details: Si 111. Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: double crystal - liquid nitrogen cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.72→35 Å / Num. obs: 62918 / % possible obs: 98.3 % / Redundancy: 6.4 % / CC1/2: 0.997 / Net I/σ(I): 13.4
Reflection shellResolution: 1.72→1.76 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2748 / CC1/2: 0.909

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P91

2p91


Resolution: 1.72→29.52 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.377 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / 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
Rfree0.2448 3142 5 %RANDOM
Rwork0.2063 ---
obs0.2082 59692 97.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 134.68 Å2 / Biso mean: 32.048 Å2 / Biso min: 14.37 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0.01 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.72→29.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4113 0 6 399 4518
Biso mean--40.1 43.14 -
Num. residues----530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0134185
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173910
X-RAY DIFFRACTIONr_angle_refined_deg1.381.6375633
X-RAY DIFFRACTIONr_angle_other_deg1.2871.5829041
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.135526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.45522.13216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.02315745
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1541528
X-RAY DIFFRACTIONr_chiral_restr0.0610.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024699
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02897
LS refinement shellResolution: 1.725→1.769 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 179 -
Rwork0.312 3710 -
all-3889 -
obs--83.12 %

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