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- PDB-1ds0: CRYSTAL STRUCTURE OF CLAVAMINATE SYNTHASE -

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Basic information

Entry
Database: PDB / ID: 1ds0
TitleCRYSTAL STRUCTURE OF CLAVAMINATE SYNTHASE
ComponentsCLAVAMINATE SYNTHASE 1
KeywordsOXIDOREDUCTASE / LYASE / Oxygenase / Trifunctional Enzyme / CLAVAMINATE SYNTHASE 1 / Jelly Roll
Function / homology
Function and homology information


clavaminate synthase / clavaminate synthase activity / clavulanic acid biosynthetic process / antibiotic biosynthetic process / iron ion binding
Similarity search - Function
: / : / Clavaminate synthase-like / Clavaminate synthase-like / Double-stranded beta-helix / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Clavaminate synthase 1
Similarity search - Component
Biological speciesStreptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.63 Å
AuthorsZhang, Z.H. / Ren, J. / Stammers, D.K. / Baldwin, J.E. / Harlos, K. / Schofield, C.J.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Structural origins of the selectivity of the trifunctional oxygenase clavaminic acid synthase.
Authors: Zhang, Z. / Ren, J. / Stammers, D.K. / Baldwin, J.E. / Harlos, K. / Schofield, C.J.
History
DepositionJan 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CLAVAMINATE SYNTHASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7635
Polymers35,4161
Non-polymers3474
Water6,431357
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.980, 67.330, 68.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CLAVAMINATE SYNTHASE 1 / CLAVAMINIC ACID SYNTHASE 1 / CAS1


Mass: 35415.785 Da / Num. of mol.: 1 / Fragment: CLAVAMINIC ACID SYNTHASE 1 (CAS1)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / References: UniProt: Q05581
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 21 ℃ / Details: macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1100 mMTris-HCl1reservoir
22 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.63→30 Å / Num. obs: 119154 / % possible obs: 93.2 % / Observed criterion σ(I): -1.5 / Redundancy: 3.28 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 27.4
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 2.61 % / Rmerge(I) obs: 0.091 / Num. unique all: 2848 / % possible all: 74.6
Reflection
*PLUS
Num. obs: 35608 / % possible obs: 91.4 % / Num. measured all: 106073 / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
% possible obs: 74.6 % / Mean I/σ(I) obs: 12.2

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.63→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.228 1797 random
Rwork0.18 --
obs-35407 -
Refinement stepCycle: LAST / Resolution: 1.63→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2482 0 19 357 2858
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_d2
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg2

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