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- PDB-6e6y: Dieckmann cyclase, NcmC -

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Basic information

Entry
Database: PDB / ID: 6e6y
TitleDieckmann cyclase, NcmC
ComponentsDieckmann cyclase, NcmC
KeywordsBIOSYNTHETIC PROTEIN / Dieckmann cyclase / off-loading / Dieckmann condensation
Function / homologyAlpha/Beta hydrolase fold / NcmC
Function and homology information
Biological speciesSaccharothrix syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsCogan, D.P. / Nair, S.K.
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Structural Basis for Enzymatic Off-Loading of Hybrid Polyketides by Dieckmann Condensation.
Authors: Cogan, D.P. / Ly, J. / Nair, S.K.
History
DepositionJul 25, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Oct 21, 2020Group: Database references / Refinement description / Category: citation / citation_author / software
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _software.name
Revision 1.3Mar 13, 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: Dieckmann cyclase, NcmC
B: Dieckmann cyclase, NcmC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8214
Polymers57,6292
Non-polymers1922
Water8,665481
1
A: Dieckmann cyclase, NcmC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9102
Polymers28,8141
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dieckmann cyclase, NcmC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9102
Polymers28,8141
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.435, 80.435, 77.923
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Dieckmann cyclase, NcmC


Mass: 28814.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharothrix syringae (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1X9WEN9
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 481 / 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: 2.19 Å3/Da / Density % sol: 43.76 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.75 M ammonium sulfate, 1.9% (w/v) PEG 400, 0.1 M HEPES pH 7.0, 3 mM DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97858 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97858 Å / Relative weight: 1
ReflectionResolution: 1.6→80.43 Å / Num. obs: 64619 / % possible obs: 99 % / Redundancy: 13.3 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 9.8
Reflection shellResolution: 1.6→1.657 Å / Rmerge(I) obs: 0.69 / Num. unique obs: 5773

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
autoPROCdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→80.43 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.603 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20396 3275 5.1 %RANDOM
Rwork0.16862 ---
obs0.17046 61355 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.263 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.18 Å2
Refinement stepCycle: 1 / Resolution: 1.6→80.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3966 0 10 481 4457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0194055
X-RAY DIFFRACTIONr_bond_other_d0.0020.023810
X-RAY DIFFRACTIONr_angle_refined_deg2.0561.9675539
X-RAY DIFFRACTIONr_angle_other_deg1.10538729
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8415533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.89522.093172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20115572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0121546
X-RAY DIFFRACTIONr_chiral_restr0.1340.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214657
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02885
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_it2.0141.5882141
X-RAY DIFFRACTIONr_mcbond_other2.0121.5872140
X-RAY DIFFRACTIONr_mcangle_it3.0352.3722671
X-RAY DIFFRACTIONr_mcangle_other3.0352.3732672
X-RAY DIFFRACTIONr_scbond_it3.0881.9171914
X-RAY DIFFRACTIONr_scbond_other3.0841.9161911
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7212.7462863
X-RAY DIFFRACTIONr_long_range_B_refined6.93820.8924658
X-RAY DIFFRACTIONr_long_range_B_other6.81420.4094551
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 214 -
Rwork0.225 3896 -
obs--84.22 %

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