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- PDB-6kvw: The complex structure of EanB/C339A/C370A and hercynine -

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Basic information

Entry
Database: PDB / ID: 6kvw
TitleThe complex structure of EanB/C339A/C370A and hercynine
ComponentsSulfurtransferase
KeywordsTRANSFERASE / complex / mutant / hercynine
Function / homology
Function and homology information


thiosulfate-cyanide sulfurtransferase activity / metal ion binding
Similarity search - Function
: / Rhodanese C-terminal signature. / Thiosulphate sulfurtransferase, conserved site / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain
Similarity search - Domain/homology
N,N,N-trimethyl-histidine / Sulfurtransferase
Similarity search - Component
Biological speciesChlorobium limicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsWu, L. / Liu, P.H. / Zhou, J.H.
CitationJournal: To Be Published
Title: The complex structure of EanB/C339A/C370A and hercynine
Authors: Wu, L. / Liu, P.H. / Zhou, J.H.
History
DepositionSep 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulfurtransferase
B: Sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,24515
Polymers104,4042
Non-polymers84113
Water9,494527
1
A: Sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6638
Polymers52,2021
Non-polymers4617
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-29 kcal/mol
Surface area18200 Å2
MethodPISA
2
B: Sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5827
Polymers52,2021
Non-polymers3806
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area18250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.823, 110.851, 120.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Sulfurtransferase


Mass: 52202.078 Da / Num. of mol.: 2 / Mutation: C339A,C370A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobium limicola (bacteria) / Strain: DSM 245 / NBRC 103803 / 6330 / Gene: Clim_1149 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: B3ECE3

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Non-polymers , 7 types, 540 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-AVJ / N,N,N-trimethyl-histidine / Hercynine


Mass: 198.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M bicine/Trizma base pH 8.5, 0.03M of each halide, 10% PEG20k 20% PEG550 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 56586 / % possible obs: 100 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.215 / Net I/σ(I): 11.5
Reflection shellResolution: 2.25→2.29 Å / Num. unique obs: 2756 / CC1/2: 0.894

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→25 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2364 2769 4.95 %
Rwork0.2173 --
obs0.2182 55980 98.86 %
Refinement stepCycle: LAST / Resolution: 2.25→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6914 0 45 527 7486

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