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- PDB-8weu: Crystal structure of Feruoyl-CoA Synthetase from Amycolatopsis th... -

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Basic information

Entry
Database: PDB / ID: 8weu
TitleCrystal structure of Feruoyl-CoA Synthetase from Amycolatopsis thermoflava
ComponentsFatty-acyl-CoA synthase
KeywordsLIGASE / Feruloyl-CoA Synthetase
Function / homology
Function and homology information


ligase activity, forming carbon-sulfur bonds / ATP binding
Similarity search - Function
: / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Fatty-acyl-CoA synthase
Similarity search - Component
Biological speciesAmycolatopsis thermoflava N1165 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSeok, J. / Kim, K.-J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural analysis of feruloyl-CoA synthetase from Amycolatopsis thermoflava
Authors: Seok, J. / Kim, K.-J.
History
DepositionSep 18, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fatty-acyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2582
Polymers53,1511
Non-polymers1061
Water2,270126
1
A: Fatty-acyl-CoA synthase
hetero molecules

A: Fatty-acyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,5154
Polymers106,3032
Non-polymers2122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_554-y+1/2,-x+1/2,-z-1/21
Buried area2740 Å2
ΔGint-10 kcal/mol
Surface area40470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.918, 134.918, 139.558
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-686-

HOH

21A-718-

HOH

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Components

#1: Protein Fatty-acyl-CoA synthase


Mass: 53151.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis thermoflava N1165 (bacteria)
Gene: EDD35_5915 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3N2H3K2
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.99 Å3/Da / Density % sol: 58.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG 3350, Ammonium sulfate, Bis-Tris

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 36835 / % possible obs: 97.4 % / Redundancy: 6.4 % / CC1/2: 0.989 / CC star: 0.997 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.039 / Rrim(I) all: 0.114 / Χ2: 5.337 / Net I/σ(I): 14.2 / Num. measured all: 236728
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.1-2.144.60.29918230.890.970.1360.3311.6597.5
2.14-2.184.70.28817880.910.9760.1280.3171.81396
2.18-2.224.90.28417900.9020.9740.1240.3122.04596.3
2.22-2.265.60.26718300.9330.9830.110.2912.26998.5
2.26-2.3150.24917980.9350.9830.1060.2732.43695.5
2.31-2.375.20.22918060.9750.9940.0960.252.70496.3
2.37-2.425.30.22117870.9550.9890.0920.2412.58996.6
2.42-2.495.50.21418140.9650.9910.0870.2332.95197
2.49-2.565.70.19617880.9680.9920.0780.2123.68796.1
2.56-2.655.80.18118190.9780.9940.0710.1953.79296.3
2.65-2.746.10.1718150.9790.9950.0640.1834.44196.8
2.74-2.856.40.15918100.9830.9960.060.1714.80297.2
2.85-2.986.80.14818380.9850.9960.0540.1585.78897.3
2.98-3.147.10.13718390.9880.9970.0490.1466.69197.3
3.14-3.337.60.12818490.990.9980.0440.1357.93298.1
3.33-3.597.90.11818720.9930.9980.0410.1258.998
3.59-3.958.30.10418980.9920.9980.0360.1119.07199.4
3.95-4.528.40.09319060.9940.9990.0320.0998.90199.5
4.52-5.78.60.08319300.9950.9990.0290.0887.299.4
5.7-508.10.06520350.9950.9990.0240.0694.80798.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data scaling
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→32.79 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.849 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25018 1874 5.1 %RANDOM
Rwork0.19994 ---
obs0.20247 34955 97.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.683 Å2
Baniso -1Baniso -2Baniso -3
1-1.64 Å2-0 Å20 Å2
2--1.64 Å2-0 Å2
3----3.28 Å2
Refinement stepCycle: 1 / Resolution: 2.1→32.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3580 0 7 126 3713
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133680
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153516
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.645014
X-RAY DIFFRACTIONr_angle_other_deg1.2971.5738078
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4725480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.24720.055181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.76815550
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9951534
X-RAY DIFFRACTIONr_chiral_restr0.0710.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024199
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02821
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4444.2721926
X-RAY DIFFRACTIONr_mcbond_other3.4444.271925
X-RAY DIFFRACTIONr_mcangle_it4.936.3932404
X-RAY DIFFRACTIONr_mcangle_other4.9296.3952405
X-RAY DIFFRACTIONr_scbond_it3.684.6021754
X-RAY DIFFRACTIONr_scbond_other3.6784.6031755
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5946.7662611
X-RAY DIFFRACTIONr_long_range_B_refined7.74850.2273909
X-RAY DIFFRACTIONr_long_range_B_other7.74850.2153901
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.152 Å
RfactorNum. reflection% reflection
Rfree0.297 134 -
Rwork0.291 2495 -
obs--94.57 %

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