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- PDB-6jdd: Crystal structure of the cypemycin decarboxylase CypD. -

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Basic information

Entry
Database: PDB / ID: 6jdd
TitleCrystal structure of the cypemycin decarboxylase CypD.
ComponentsCypemycin cysteine dehydrogenase (decarboxylating)
KeywordsBIOSYNTHETIC PROTEIN / Decarboxylase / RiPP / Linaridin
Function / homology
Function and homology information


cypemycin cysteine dehydrogenase (decarboxylating) / peptide antibiotic biosynthetic process / carboxy-lyase activity / oxidoreductase activity
Similarity search - Function
: / Flavoprotein / Flavin prenyltransferase-like / Flavoprotein
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Cypemycin cysteine dehydrogenase (decarboxylating)
Similarity search - Component
Biological speciesStreptomyces sp (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsZhang, Q. / Yuan, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670060 China
CitationJournal: FEBS Lett. / Year: 2019
Title: Convergent evolution of the Cys decarboxylases involved in aminovinyl-cysteine (AviCys) biosynthesis.
Authors: Mo, T. / Yuan, H. / Wang, F. / Ma, S. / Wang, J. / Li, T. / Liu, G. / Yu, S. / Tan, X. / Ding, W. / Zhang, Q.
History
DepositionFeb 1, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _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: Cypemycin cysteine dehydrogenase (decarboxylating)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8755
Polymers20,7721
Non-polymers1,1044
Water91951
1
A: Cypemycin cysteine dehydrogenase (decarboxylating)
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)262,50660
Polymers249,25912
Non-polymers13,24748
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation26_555-x,-y,z1
crystal symmetry operation31_555-z,-x,y1
crystal symmetry operation36_555-y,-z,x1
crystal symmetry operation52_555x,-y,-z1
crystal symmetry operation54_555z,-x,-y1
crystal symmetry operation59_555y,-z,-x1
crystal symmetry operation75_555-x,y,-z1
crystal symmetry operation80_555-z,x,-y1
crystal symmetry operation82_555-y,z,-x1
Buried area40120 Å2
ΔGint-226 kcal/mol
Surface area75010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)229.456, 229.456, 229.456
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132

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Components

#1: Protein Cypemycin cysteine dehydrogenase (decarboxylating)


Mass: 20771.584 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp (bacteria) / Gene: cypD / Plasmid: pET28a / Production host: Enterobacteria phage L1 (virus)
References: UniProt: E5KIB9, cypemycin cysteine dehydrogenase (decarboxylating)
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 6.06 Å3/Da / Density % sol: 75.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 50 mM NaCl, 0.1 M Imidazole, 10 mM Tris, pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 16495 / % possible obs: 100 % / Redundancy: 18.7 % / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.044 / Net I/σ(I): 26.8
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 19.4 % / Rmerge(I) obs: 0.844 / Mean I/σ(I) obs: 3.58 / Num. unique obs: 794 / CC1/2: 0.92 / Rpim(I) all: 0.196 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→44.2 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.912 / SU B: 12.55 / SU ML: 0.119 / Cross valid method: FREE R-VALUE / ESU R: 0.374 / ESU R Free: 0.179
RfactorNum. reflection% reflectionSelection details
Rfree0.2193 831 5.1 %RANDOM
Rwork0.1724 ---
obs0.17469 15611 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 49.259 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.6→44.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1359 0 74 51 1484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0131474
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171361
X-RAY DIFFRACTIONr_angle_refined_deg2.0011.72016
X-RAY DIFFRACTIONr_angle_other_deg1.4471.6163145
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1745176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.17721.33375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.64115219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0661512
X-RAY DIFFRACTIONr_chiral_restr0.0990.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021615
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02310
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_it8.1195.083707
X-RAY DIFFRACTIONr_mcbond_other8.1015.071706
X-RAY DIFFRACTIONr_mcangle_it9.727.593882
X-RAY DIFFRACTIONr_mcangle_other9.7167.607883
X-RAY DIFFRACTIONr_scbond_it9.3745.457767
X-RAY DIFFRACTIONr_scbond_other9.3725.458768
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.4677.9861135
X-RAY DIFFRACTIONr_long_range_B_refined9.56856.9571718
X-RAY DIFFRACTIONr_long_range_B_other9.56956.9691719
X-RAY DIFFRACTIONr_rigid_bond_restr4.23632835
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.601→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 64 -
Rwork0.207 1123 -
obs--100 %

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