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- PDB-3s8m: The Crystal Structure of FabV -

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Basic information

Entry
Database: PDB / ID: 3s8m
TitleThe Crystal Structure of FabV
ComponentsEnoyl-ACP Reductase
KeywordsOXIDOREDUCTASE / ROSSMANN FOLD / NADH Binding / FATTY ACID SYNTHESIS / enoyl-ACP
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) / 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 speciesXanthomonas oryzae pv. oryzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsLi, H. / Zhang, X.L. / Bi, L.J. / He, J. / Jiang, T.
CitationJournal: Plos One / Year: 2011
Title: Determination of the Crystal Structure and Active Residues of FabV, the Enoyl-ACP Reductase from Xanthomonas oryzae.
Authors: Li, H. / Zhang, X. / Bi, L. / He, J. / Jiang, T.
History
DepositionMay 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enoyl-ACP Reductase


Theoretical massNumber of molelcules
Total (without water)46,2471
Polymers46,2471
Non-polymers00
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.52, 74.53, 107.39
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Enoyl-ACP Reductase


Mass: 46247.066 Da / Num. of mol.: 1 / Mutation: E192D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas oryzae pv. oryzae (bacteria)
Strain: KS-1-21 / Gene: Xanthomonas oryzae, XOO0026 / Plasmid: pET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: Q2P9J6, Oxidoreductases; Acting on the CH-CH group of donors; With NAD+ or NADP+ as acceptor
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAUTHORS STATE THAT THE FIRST TWO METHIONINES WERE NOT SEEN IN THE STRUCTURE. THEREFORE, COULD NOT ...AUTHORS STATE THAT THE FIRST TWO METHIONINES WERE NOT SEEN IN THE STRUCTURE. THEREFORE, COULD NOT BE POSSIBLE TO CONCLUDE WHERE THOSE WERE MET OR MSE. D192 IS A NATURAL MUTATION WHICH MAY BE SPECIES-SPECIFIC.

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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: 2.19 Å3/Da / Density % sol: 43.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM Bis-Tris, 200 mM NaCl, 1 mM DTT and 15% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.97902, 0.97930
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 20, 2010
RadiationMonochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979021
20.97931
ReflectionResolution: 1.6→19.89 Å / Num. all: 53994 / Num. obs: 53994 / % possible obs: 99.5 % / Observed criterion σ(F): 2.13 / Redundancy: 14.3 % / Rmerge(I) obs: 0.06 / Rsym value: 0.205 / Net I/σ(I): 64.1
Reflection shellResolution: 1.6→1.66 Å / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 14.3 / Rsym value: 0.068 / % possible all: 99.9

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Processing

Software
NameClassification
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→19.89 Å / SU ML: 0.14 / σ(F): 2.13 / Phase error: 17.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2051 2000 3.7 %RANDOM
Rwork0.1852 ---
obs0.1859 53994 99.53 %-
all-53994 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.022 Å2 / ksol: 0.364 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.0597 Å2-0 Å2-0 Å2
2---2.6693 Å20 Å2
3----2.3903 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2983 0 0 277 3260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063040
X-RAY DIFFRACTIONf_angle_d1.0094122
X-RAY DIFFRACTIONf_dihedral_angle_d14.8731082
X-RAY DIFFRACTIONf_chiral_restr0.071462
X-RAY DIFFRACTIONf_plane_restr0.005536
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.6-1.65720.1871960.14715090528699
1.6572-1.72350.19961970.16395110530799
1.7235-1.80190.21241980.16895148534699
1.8019-1.89680.19881970.172251255322100
1.8968-2.01550.1971990.183551905389100
2.0155-2.1710.19171980.183651605358100
2.171-2.38910.22612010.186452185419100
2.3891-2.73410.21822020.197452385440100
2.7341-3.44170.22332030.206652755478100
3.4417-19.89160.18392090.17455440564999

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