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- PDB-6vwr: X-ray structure of clavaminate synthase with vanadyl, succinate, ... -

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Basic information

Entry
Database: PDB / ID: 6vwr
TitleX-ray structure of clavaminate synthase with vanadyl, succinate, and deoxyguanidinoproclavaminic acid
ComponentsClavaminate synthase 3
KeywordsOXIDOREDUCTASE / iron / oxygenase / hydroxylase / oxacyclase / desaturase / alpha-ketoglutarate
Function / homology
Function and homology information


antibiotic biosynthetic process / oxidoreductase activity / iron ion binding
Similarity search - Function
: / : / Clavaminate synthase-like / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily
Similarity search - Domain/homology
DEOXYGUANIDINOPROCLAVAMINIC ACID / SUCCINIC ACID / oxovanadium(2+) / Clavaminate synthase 3
Similarity search - Component
Biological speciesStreptomyces antibioticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBoal, A.K. / Vavra, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: X-ray structure of clavaminate synthase with vanadyl, succinate, and deoxyguanidinoproclavaminic acid
Authors: Vavra, J. / Dunham, N.P. / Krebs, C. / Boal, A.K. / Bollinger, J.M.
History
DepositionFeb 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Clavaminate synthase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7834
Polymers38,3701
Non-polymers4133
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint10 kcal/mol
Surface area13060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.288, 79.288, 105.573
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Clavaminate synthase 3


Mass: 38370.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces antibioticus (bacteria) / Gene: cas3
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: I0CBY7, clavaminate synthase
#2: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#3: Chemical ChemComp-PCX / DEOXYGUANIDINOPROCLAVAMINIC ACID


Mass: 228.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N4O3
#4: Chemical ChemComp-VVO / oxovanadium(2+)


Mass: 66.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: OV
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: magnesium acetate, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03314 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 7, 2019
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03314 Å / Relative weight: 1
ReflectionResolution: 1.5→63.4 Å / Num. obs: 53542 / % possible obs: 98.8 % / Redundancy: 11.6 % / Biso Wilson estimate: 14.4 Å2 / Net I/σ(I): 33.37
Reflection shellResolution: 1.5→1.53 Å

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Processing

Software
NameClassification
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1DRT

1drt


Resolution: 1.5→50 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35
RfactorNum. reflection% reflection
Rfree0.196 1998 3.89 %
Rwork0.175 --
obs-51368 99.9 %
Displacement parametersBiso mean: 18.71 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2523 0 26 415 2964
LS refinement shellResolution: 1.53→1.57 Å
RfactorNum. reflection% reflection
Rfree0.2701 140 -
Rwork0.2884 3456 -
obs--99.81 %

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