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- PDB-5wsx: The crystal structure of SAV606 -

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Basic information

Entry
Database: PDB / ID: 5wsx
TitleThe crystal structure of SAV606
ComponentsUncharacterized protein
KeywordsHYDROLASE / thioesterase / hotdog fold
Function / homology(3R)-3-[(carboxylmethyl)amino]fatty acid synthase / Long-chain fatty acyl-CoA thioesterase FcoT-like / Long-chain fatty acyl-CoA thioesterase, Rv0098-like superfamily / FcoT-like thioesterase domain / fatty acid metabolic process / lyase activity / (2E)-enoyl-[ACP] glycyltransferase
Function and homology information
Biological speciesStreptomyces avermitilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsChisuga, T. / Miyanaga, A. / Kudo, F. / Eguchi, T.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural analysis of the dual-function thioesterase SAV606 unravels the mechanism of Michael addition of glycine to an alpha , beta-unsaturated thioester.
Authors: Chisuga, T. / Miyanaga, A. / Kudo, F. / Eguchi, T.
History
DepositionDec 8, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 8, 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)43,0072
Polymers43,0072
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2110 Å2
ΔGint-9 kcal/mol
Surface area14830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.880, 50.100, 125.010
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 Uncharacterized protein / thioesterase


Mass: 21503.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680) (bacteria)
Strain: ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680
Gene: SAVERM_606 / Plasmid: pCold I / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q79ZR9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.82 Å3/Da / Density % sol: 32.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 1.0 M Magnesium citrate, 0.1 M imidazole, 1% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 28, 2015
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 12859 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.137 / Net I/σ(I): 10.8
Reflection shellResolution: 2.4→2.52 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PFC

2pfc


Resolution: 2.4→46.55 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.911 / SU B: 18.801 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.607 / ESU R Free: 0.295 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26113 625 4.9 %RANDOM
Rwork0.2046 ---
obs0.20728 12191 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.442 Å2
Baniso -1Baniso -2Baniso -3
1-1.76 Å20 Å2-0 Å2
2--0.25 Å2-0 Å2
3----2.01 Å2
Refinement stepCycle: 1 / Resolution: 2.4→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2540 0 0 67 2607
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192604
X-RAY DIFFRACTIONr_bond_other_d0.0010.022400
X-RAY DIFFRACTIONr_angle_refined_deg1.5971.9373527
X-RAY DIFFRACTIONr_angle_other_deg0.83.0015491
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9555307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.00422.667135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.52815415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6841525
X-RAY DIFFRACTIONr_chiral_restr0.0840.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212931
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02652
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 45 -
Rwork0.273 874 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.33510.06850.47370.33470.14160.7039-0.03020.02790.03360.02180.01880.0185-0.04450.03470.01140.00760.0008-0.00770.00520.00220.174920.04148.375724.3679
20.55160.24150.05990.9931-0.14140.87910.04160.0827-0.0194-0.0654-0.01010.075-0.0183-0.0747-0.03150.01280.0149-0.00950.0265-0.02010.14784.8585-5.03087.1045
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 169
2X-RAY DIFFRACTION2B5 - 168

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