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- PDB-6isl: SnoaL-like cyclase XimE with its product xiamenmycin B -

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Basic information

Entry
Database: PDB / ID: 6isl
TitleSnoaL-like cyclase XimE with its product xiamenmycin B
ComponentsXimE, SnoaL-like domain protein
KeywordsLYASE / SnoaL-like cyslase XimE
Function / homologySnoaL-like domain / SnoaL-like domain / NTF2-like domain superfamily / Chem-XIA / XimE
Function and homology information
Biological speciesStreptomyces xiamenensis 318 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.77 Å
AuthorsHe, B. / Zhou, T. / Bu, X. / Weng, J. / Xu, J. / Lin, S. / Zheng, J. / Zhao, Y. / Xu, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China81473105 China
CitationJournal: Acs Catalysis / Year: 2019
Title: Enzymatic Pyran Formation Involved in Xiamenmycin Biosynthesis
Authors: He, B. / Zhou, T. / Bu, X. / Weng, J. / Xu, J. / Lin, S. / Zheng, J. / Zhao, Y. / Xu, M.
History
DepositionNov 16, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: XimE, SnoaL-like domain protein
B: XimE, SnoaL-like domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9914
Polymers34,4112
Non-polymers5812
Water1,04558
1
A: XimE, SnoaL-like domain protein
hetero molecules

B: XimE, SnoaL-like domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9914
Polymers34,4112
Non-polymers5812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area1540 Å2
ΔGint-6 kcal/mol
Surface area11620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.220, 80.220, 112.200
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein XimE, SnoaL-like domain protein


Mass: 17205.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces xiamenensis 318 (bacteria)
Gene: ximE / Plasmid: pET28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: U5Q2N8, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases
#2: Chemical ChemComp-XIA / (2R,3S)-2-methyl-2-(4-methylpent-3-enyl)-3-oxidanyl-3,4-dihydrochromene-6-carboxylic acid / xiamenmycin B


Mass: 290.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H22O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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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: 2.02 Å3/Da / Density % sol: 39.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 2M xiamenmycin B, 0.2M malonic acid, 20% PEG 3350, pH 4.5
PH range: 3.8-5.5 / Temp details: 293

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.77→59.1 Å / Num. obs: 24399 / % possible obs: 100 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 12.7
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
PDB_EXTRACT3.24data extraction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.77→59.07 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.937 / SU B: 2.669 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.113
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2205 1243 4.8 %RANDOM
Rwork0.1953 ---
obs0.1966 24399 97.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 120.95 Å2 / Biso mean: 21.267 Å2 / Biso min: 7.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0.04 Å20 Å2
2---0.08 Å20 Å2
3---0.26 Å2
Refinement stepCycle: final / Resolution: 1.77→59.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1858 0 42 58 1958
Biso mean--20.46 31.43 -
Num. residues----240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191942
X-RAY DIFFRACTIONr_bond_other_d0.0020.021794
X-RAY DIFFRACTIONr_angle_refined_deg1.9871.9692660
X-RAY DIFFRACTIONr_angle_other_deg1.09734112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1755238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.07822.14384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.08515288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7271520
X-RAY DIFFRACTIONr_chiral_restr0.1220.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212160
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02416
LS refinement shellResolution: 1.77→1.816 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 89 -
Rwork0.233 1569 -
all-1658 -
obs--84.12 %

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