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- PDB-5x7l: Structure of TsrD from Streptomyces laurentii -

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Basic information

Entry
Database: PDB / ID: 5x7l
TitleStructure of TsrD from Streptomyces laurentii
ComponentsTsrD
KeywordsISOMERASE / Tsrd / TsrE / Streptomyces laurentii
Function / homologypolyketide metabolic process / SnoaL-like polyketide cyclase / Polyketide cyclase SnoaL-like / NTF2-like domain superfamily / ISOPROPYL ALCOHOL / TsrD
Function and homology information
Biological speciesStreptomyces laurentii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.22 Å
AuthorsSong, Y. / Lin, Z. / Deng, W. / Liu, W.
Funding support China, 3items
OrganizationGrant numberCountry
NSFC31430005, 21520102004, 21472231 and 21621002 China
STCSM14JC1407700 and 15JC1400400 China
CASXDB20020200 China
CitationJournal: To Be Published
Title: Structure of TsrD from Streptomyces laurentii
Authors: Song, Y. / Lin, Z. / Deng, W. / Liu, W.
History
DepositionFeb 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: TsrD
B: TsrD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5237
Polymers31,2222
Non-polymers3005
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-11 kcal/mol
Surface area12110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.232, 54.232, 199.952
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-203-

IPA

21A-305-

HOH

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Components

#1: Protein TsrD / TsrS


Mass: 15611.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces laurentii (bacteria) / Gene: tsrD / Production host: Escherichia coli (E. coli) / References: UniProt: C0JRY3
#2: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.75 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES sodium pH 7.5, and 30% v/v 2-Propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: AREA DETECTOR / Date: Apr 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.22→50 Å / Num. obs: 102592 / % possible obs: 99.6 % / Redundancy: 18.9 % / Net I/σ(I): 38.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-3000data processing
RefinementMethod to determine structure: SAD / Resolution: 1.22→38.42 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.917 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.033 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16631 5013 5 %RANDOM
Rwork0.15062 ---
obs0.1514 95308 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.411 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0.08 Å20 Å2
2---0.08 Å20 Å2
3---0.26 Å2
Refinement stepCycle: 1 / Resolution: 1.22→38.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2091 0 20 337 2448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0192157
X-RAY DIFFRACTIONr_bond_other_d0.0020.022086
X-RAY DIFFRACTIONr_angle_refined_deg0.9781.9762916
X-RAY DIFFRACTIONr_angle_other_deg1.43934766
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7765269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.20822.6100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.01215328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8421523
X-RAY DIFFRACTIONr_chiral_restr0.0520.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212430
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02507
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_it0.8351.5341076
X-RAY DIFFRACTIONr_mcbond_other0.8431.5311075
X-RAY DIFFRACTIONr_mcangle_it1.2172.3021342
X-RAY DIFFRACTIONr_mcangle_other1.2212.3061343
X-RAY DIFFRACTIONr_scbond_it1.0331.6851078
X-RAY DIFFRACTIONr_scbond_other1.0331.6851079
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.3682.4751571
X-RAY DIFFRACTIONr_long_range_B_refined2.40413.9222607
X-RAY DIFFRACTIONr_long_range_B_other2.40413.9262608
X-RAY DIFFRACTIONr_rigid_bond_restr1.90534236
X-RAY DIFFRACTIONr_sphericity_free20.3965108
X-RAY DIFFRACTIONr_sphericity_bonded7.53654429
LS refinement shellResolution: 1.221→1.253 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.174 353 -
Rwork0.146 6612 -
obs--93.21 %

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