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- PDB-1rxg: DEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH FE(II) AND 2-OXO... -

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Basic information

Entry
Database: PDB / ID: 1rxg
TitleDEACETOXYCEPHALOSPORIN C SYNTHASE COMPLEXED WITH FE(II) AND 2-OXOGLUTARATE
ComponentsDEACETOXYCEPHALOSPORIN C SYNTHASE
KeywordsOXIDOREDUCTASE / FERROUS OXYGENASE / CEPHALOSPORIN / 2-OXOGLUTARATE / ANTIBIOTICS / MEROHEDRAL TWINNING
Function / homology
Function and homology information


deacetoxycephalosporin-C synthase / deacetoxycephalosporin-C synthase activity / L-ascorbic acid binding / antibiotic biosynthetic process / iron ion binding
Similarity search - Function
: / Isopenicillin N synthase, conserved site / Isopenicillin N synthase signature 2. / B-lactam Antibiotic, Isopenicillin N Synthase; Chain / non-haem dioxygenase in morphine synthesis N-terminal / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. ...: / Isopenicillin N synthase, conserved site / Isopenicillin N synthase signature 2. / B-lactam Antibiotic, Isopenicillin N Synthase; Chain / non-haem dioxygenase in morphine synthesis N-terminal / Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / Oxoglutarate/iron-dependent dioxygenase / Fe(2+) 2-oxoglutarate dioxygenase domain profile. / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-OXOGLUTARIC ACID / : / Deacetoxycephalosporin C synthase
Similarity search - Component
Biological speciesStreptomyces clavuligerus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.5 Å
AuthorsValegard, K. / Terwisscha Van Scheltinga, A.C. / Lloyd, M.D. / Hara, T. / Ramaswamy, S. / Perrakis, A. / Thompson, A. / Lee, H.J. / Baldwin, J.E. / Shofield, C.J. ...Valegard, K. / Terwisscha Van Scheltinga, A.C. / Lloyd, M.D. / Hara, T. / Ramaswamy, S. / Perrakis, A. / Thompson, A. / Lee, H.J. / Baldwin, J.E. / Shofield, C.J. / Hajdu, J. / Andersson, I.
Citation
#1: Journal: Bioorg.Med.Chem.Lett. / Year: 1994
Title: Substrate Specificity of Recombinant Streptomyces Clavuligerus Deacetoxycephalosporin C Synthase
Authors: Morgan, N. / Pereira, I.A.C. / Andersson, I. / Adlington, R.M. / Baldwin, J.E. / Cole, S.E. / Crouch, N.P. / Sutherland, J.D.
History
DepositionJun 5, 1998Processing site: BNL
Revision 1.0Jun 8, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site
Revision 1.4Mar 10, 2021Group: Advisory / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_conn_angle ...pdbx_distant_solvent_atoms / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 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: DEACETOXYCEPHALOSPORIN C SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8904
Polymers34,5921
Non-polymers2983
Water5,350297
1
A: DEACETOXYCEPHALOSPORIN C SYNTHASE
hetero molecules

A: DEACETOXYCEPHALOSPORIN C SYNTHASE
hetero molecules

A: DEACETOXYCEPHALOSPORIN C SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,66912
Polymers103,7753
Non-polymers8949
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area10570 Å2
ΔGint-105 kcal/mol
Surface area30130 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)107.700, 107.700, 71.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-668-

HOH

21A-694-

HOH

31A-706-

HOH

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Components

#1: Protein DEACETOXYCEPHALOSPORIN C SYNTHASE / RING EXPANDING ENZYME / RING EXPANDASE


Mass: 34591.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces clavuligerus (bacteria) / Plasmid: PET 11A / Production host: Escherichia coli (E. coli) / Strain (production host): PET / References: UniProt: P18548
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.6 Å3/Da / Density % sol: 54 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Method: unknown / PH range low: 7.5 / PH range high: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.75 Mammonium sulfate11
25 mM2-oxoglutarate11
30.1 MHEPES11

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.8
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1998
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.5→16 Å / Num. obs: 42718 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 14.3
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 5 / Rsym value: 0.256 / % possible all: 99.7
Reflection shell
*PLUS
% possible obs: 99.7 %

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Processing

Software
NameClassification
SHELXL-97model building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-97phasing
RefinementMethod to determine structure: MIR / Resolution: 1.5→20 Å / Num. parameters: 20351 / Num. restraintsaints: 25242 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: REFINED AGAINST MEROHEDRALLY TWINNED INTENSITIES
RfactorNum. reflection% reflectionSelection details
Rfree0.156 910 2 %RANDOM
obs0.125 -97.6 %-
all-48010 --
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 2 / Occupancy sum hydrogen: 2072 / Occupancy sum non hydrogen: 2363.3
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2157 0 16 297 2470
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.362
X-RAY DIFFRACTIONs_zero_chiral_vol0.048
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.059
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.038
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.053
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refine LS restraints
*PLUS
Type: s_chiral_restr / Dev ideal: 0.059

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