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- PDB-1unb: Deacetoxycephalosporin C synthase complexed with 2-oxoglutarate a... -

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Basic information

Entry
Database: PDB / ID: 1unb
TitleDeacetoxycephalosporin C synthase complexed with 2-oxoglutarate and ampicillin
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
: / 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 / : / Chem-PN1 / Deacetoxycephalosporin C synthase
Similarity search - Component
Biological speciesSTREPTOMYCES CLAVULIGERUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 9, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 / _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

Downloads & links

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Assembly

Deposited unit
A: DEACETOXYCEPHALOSPORIN C SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1434
Polymers34,5921
Non-polymers5513
Water3,387188
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)105,42912
Polymers103,7753
Non-polymers1,6549
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area11480 Å2
ΔGint-59.54 kcal/mol
Surface area31140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.700, 106.700, 71.600
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-2066-

HOH

21A-2067-

HOH

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Components

#1: Protein DEACETOXYCEPHALOSPORIN C SYNTHETASE / EXPANDASE / DAOCS


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-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-PN1 / (2S,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID


Mass: 349.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H19N3O4S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.26 Å3/Da / Density % sol: 45.7 %
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: 1.076
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.076 Å / Relative weight: 1
ReflectionResolution: 1.5→31.4 Å / Num. obs: 45847 / % possible obs: 94 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.064
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.295 / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.5 Å / Num. obs: 45862 / % possible obs: 94.2 % / Num. measured all: 299664 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.312

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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: 1.5→31.5 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.76 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE RESIDUES MISSING IN THE PDB ENTRY (81-90,167-177 AND 310-311) ARE DISORDERED, AND THEREFORE OMITTED FROM THE MODEL
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2132 5.1 %RANDOM
Rwork0.189 ---
obs0.191 40046 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: 22.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0.33 Å20 Å2
2---0.66 Å20 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.5→31.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2233 0 35 188 2456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0212400
X-RAY DIFFRACTIONr_bond_other_d0.0230.022130
X-RAY DIFFRACTIONr_angle_refined_deg2.3751.963276
X-RAY DIFFRACTIONr_angle_other_deg1.94334931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1545306
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_restr0.1450.2359
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022737
X-RAY DIFFRACTIONr_gen_planes_other0.010.02553
X-RAY DIFFRACTIONr_nbd_refined0.2320.2517
X-RAY DIFFRACTIONr_nbd_other0.2680.22535
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1020.21402
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2125
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1250.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2940.2100
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4641.51467
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.47222369
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.283933
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.1694.5894
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: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.314 168
Rwork0.283 3052
Refinement
*PLUS
Highest resolution: 1.5 Å / Rfactor Rfree: 0.237 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

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