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- PDB-1uog: Deacetoxycephalosporin C synthase complexed with deacetoxycephalo... -

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Basic information

Entry
Database: PDB / ID: 1uog
TitleDeacetoxycephalosporin C synthase complexed with deacetoxycephalosporin C
ComponentsDEACETOXYCEPHALOSPORIN C SYNTHETASE
KeywordsOXIDOREDUCTASE / ANTIBIOTIC BIOSYNTHESIS
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
B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Isopenicillin N synthase, conserved site / Isopenicillin N synthase signature 2. / 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 ...B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Isopenicillin N synthase, conserved site / Isopenicillin N synthase signature 2. / 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
: / DEACETOXYCEPHALOSPORIN-C / Deacetoxycephalosporin C synthase
Similarity search - Component
Biological speciesSTREPTOMYCES CLAVULIGERUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsValegard, K. / Terwisscha van Scheltinga, A.C. / Dubus, A. / Oster, L.M. / Rhangino, G. / Hajdu, J. / Andersson, I.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: The Structural Basis of Cephalosporin Formation in a Mononuclear Ferrous Enzyme
Authors: Valegard, K. / Terwisscha van Scheltinga, A.C. / Dubus, A. / Ranghino, G. / Oster, L.M. / Hajdu, J. / Andersson, I.
History
DepositionSep 17, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / diffrn_source
Item: _audit_author.name / _citation.page_last ..._audit_author.name / _citation.page_last / _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DEACETOXYCEPHALOSPORIN C SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0053
Polymers34,5921
Non-polymers4132
Water2,180121
1
A: DEACETOXYCEPHALOSPORIN C SYNTHETASE
hetero molecules

A: DEACETOXYCEPHALOSPORIN C SYNTHETASE
hetero molecules

A: DEACETOXYCEPHALOSPORIN C SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,0159
Polymers103,7753
Non-polymers1,2406
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
MethodPQS
Unit cell
Length a, b, c (Å)106.600, 106.600, 74.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein DEACETOXYCEPHALOSPORIN C SYNTHETASE / DAOCS / EXPANDASE


Mass: 34591.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Plasmid: PET11A / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P18548, deacetoxycephalosporin-C synthase
#2: Chemical ChemComp-P1C / DEACETOXYCEPHALOSPORIN-C


Mass: 357.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H19N3O6S
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 53 %
Description: THE DATA WERE COLLECTED FROM A MEROHEDRALLY TWINNED CRYSTAL
Crystal growpH: 7.5
Details: 1.75M AMMONIUM SULPHATE, 5MM 2-OXOGLUTARATE,0.1M HEPESPH7.5, pH 7.50
Crystal grow
*PLUS
Method: unknown / Details: Valegard, K., (1998) Nature, 394, 805. / 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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.965
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 1.7→25.4 Å / Num. obs: 31415 / % possible obs: 91 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.046
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.186 / % possible all: 99.5
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. measured all: 192826 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 99.5 % / Rmerge(I) obs: 0.186

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RXF

1rxf


Resolution: 1.7→25.4 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.624 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: REFINED AGAINST DETWINNED DATA THE RESIDUES MISSING IN THE PDB ENTRY (1, 81-97,165-180, 196-203 247-258 AND 311) ARE DISORDERED, AND THEREFORE OMITTED FROM THE MODEL
RfactorNum. reflection% reflectionSelection details
Rfree0.242 1392 5 %RANDOM
Rwork0.204 ---
obs0.206 26307 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å2-0.4 Å20 Å2
2---0.8 Å20 Å2
3---1.21 Å2
Refinement stepCycle: LAST / Resolution: 1.7→25.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1994 0 25 121 2140
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0212063
X-RAY DIFFRACTIONr_bond_other_d0.0040.021828
X-RAY DIFFRACTIONr_angle_refined_deg2.3651.9562797
X-RAY DIFFRACTIONr_angle_other_deg1.03634222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4325251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1250.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022313
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02464
X-RAY DIFFRACTIONr_nbd_refined0.2320.2405
X-RAY DIFFRACTIONr_nbd_other0.2630.22079
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0940.21202
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2620.291
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1290.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2710.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3120.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.7740.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.90931266
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.3252030
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.3146797
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.6168765
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.292 121
Rwork0.215 2195
Refinement
*PLUS
Highest resolution: 1.7 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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