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- PDB-6isk: SnoaL-like cyclase XimE -

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Basic information

Entry
Database: PDB / ID: 6isk
TitleSnoaL-like cyclase XimE
ComponentsXimE, SnoaL-like domain protein
KeywordsLYASE / Snoal-like cyclase
Function / homologySnoaL-like domain / SnoaL-like domain / NTF2-like domain superfamily / MALONIC ACID / 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
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.title / _citation.year
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)34,7856
Polymers34,4112
Non-polymers3744
Water93752
1
A: XimE, SnoaL-like domain protein
hetero molecules

B: XimE, SnoaL-like domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7856
Polymers34,4112
Non-polymers3744
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area2780 Å2
ΔGint-20 kcal/mol
Surface area11530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.894, 79.894, 111.721
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-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C3H4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 1.99 Å3/Da / Density % sol: 38.32 % / Description: Starked layers of thin slices.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 0.2M malonic acid, 22% PEG 3350, pH 4.0 / PH range: 3.8-4.5 / 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 22, 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 Å / Num. obs: 25607 / % possible obs: 97.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 15.4
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.438 / % possible all: 83

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Processing

Software
NameVersionClassification
HKL-3000v1.0data reduction
REFMAC5.8.0158refinement
PDB_EXTRACT3.24data extraction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.77→58.82 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.912 / SU B: 2.763 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.122
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2424 1363 5.2 %RANDOM
Rwork0.2103 ---
obs0.212 24732 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 74.7 Å2 / Biso mean: 23.098 Å2 / Biso min: 9.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å2-0.23 Å20 Å2
2---0.46 Å20 Å2
3---1.48 Å2
Refinement stepCycle: final / Resolution: 1.77→58.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1869 0 14 52 1935
Biso mean--34.23 26.69 -
Num. residues----242
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0191918
X-RAY DIFFRACTIONr_bond_other_d0.0010.021768
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.9542616
X-RAY DIFFRACTIONr_angle_other_deg0.73934056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.665237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.28722.14384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.54515288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3091520
X-RAY DIFFRACTIONr_chiral_restr0.1030.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0212141
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02408
LS refinement shellResolution: 1.766→1.812 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 93 -
Rwork0.262 1861 -
all-1954 -
obs--99.95 %

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