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- PDB-6e6u: Variant C89S of Dieckmann cyclase, NcmC -

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Basic information

Entry
Database: PDB / ID: 6e6u
TitleVariant C89S of Dieckmann 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 / MOLECULAR REPLACEMENT / Resolution: 1.55 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 1.3Oct 11, 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

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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)57,7894
Polymers57,5972
Non-polymers1922
Water9,350519
1
A: Dieckmann cyclase, NcmC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8942
Polymers28,7981
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)28,8942
Polymers28,7981
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.361, 80.361, 78.323
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: 28798.316 Da / Num. of mol.: 2 / Mutation: C89S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharothrix syringae (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1X9WEN9
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 519 / 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: 2.2 Å3/Da / Density % sol: 43.97 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.7 M ammonium sulfate, 2.5% PEG 400, 0.1 M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.55→80.36 Å / Num. obs: 71503 / % possible obs: 99.4 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 16.8
Reflection shellResolution: 1.552→1.557 Å / Rmerge(I) obs: 1.141

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E6Y

6e6y


Resolution: 1.55→80.36 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.629 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21508 3570 5 %RANDOM
Rwork0.17318 ---
obs0.17518 67900 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å2-0 Å2-0 Å2
2--0.41 Å2-0 Å2
3----0.82 Å2
Refinement stepCycle: 1 / Resolution: 1.55→80.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3936 0 10 519 4465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0194022
X-RAY DIFFRACTIONr_bond_other_d0.0020.023784
X-RAY DIFFRACTIONr_angle_refined_deg2.0841.9675491
X-RAY DIFFRACTIONr_angle_other_deg1.15838663
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9165528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3922170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87915569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2311546
X-RAY DIFFRACTIONr_chiral_restr0.1390.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0214620
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02882
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_it2.3222.1182124
X-RAY DIFFRACTIONr_mcbond_other2.322.1172123
X-RAY DIFFRACTIONr_mcangle_it3.243.1672648
X-RAY DIFFRACTIONr_mcangle_other3.2413.1672649
X-RAY DIFFRACTIONr_scbond_it3.4772.4741898
X-RAY DIFFRACTIONr_scbond_other3.4612.4721890
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0923.5642831
X-RAY DIFFRACTIONr_long_range_B_refined8.42127.8854651
X-RAY DIFFRACTIONr_long_range_B_other7.46526.664448
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.552→1.592 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 296 -
Rwork0.254 4997 -
obs--99.89 %

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