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- PDB-1w2n: Deacetoxycephalosporin C synthase (with a N-terminal his-tag) in ... -

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Basic information

Entry
Database: PDB / ID: 1w2n
TitleDeacetoxycephalosporin C synthase (with a N-terminal his-tag) in complex with Fe(II) and ampicillin
ComponentsDEACETOXYCEPHALOSPORIN C SYNTHASE
KeywordsOXIDOREDUCTASE / CEPHALOSPORIN / PENICILLIN / MONONUCLEAR FERROUS ENZYMES / 2-OXOGLUTARATE DEPENDENT OXYGENASES / 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
: / Chem-PN1 / Deacetoxycephalosporin C synthase
Similarity search - Component
Biological speciesSTREPTOMYCES CLAVULIGERUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.7 Å
AuthorsOster, L.M. / Terwisscha Van Scheltinga, A.C. / Valegard, K. / Mackenzie Hose, A. / Dubus, A. / Hajdu, J. / Andersson, I.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Conformational Flexibility of the C Terminus with Implications for Substrate Binding and Catalysis Revealed in a New Crystal Form of Deacetoxycephalosporin C Synthase
Authors: Oster, L.M. / Terwisscha Van Scheltinga, A.C. / Valegard, K. / Mackenzie Hose, A. / Dubus, A. / Hajdu, J. / Andersson, I.
History
DepositionJul 7, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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.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.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

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Assembly

Deposited unit
A: DEACETOXYCEPHALOSPORIN C SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1683
Polymers36,7631
Non-polymers4052
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)138.800, 138.800, 48.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein DEACETOXYCEPHALOSPORIN C SYNTHASE / DAOCS / EXPANDASE


Mass: 36762.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Plasmid: PET-15B / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P18548, EC: 1.14.10.1
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE ENZYME WAS EXPRESSED WITH A N-TERMINAL HIS-TAG

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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: 4.1 Å3/Da / Density % sol: 70 %
Crystal growpH: 8 / Details: 100 MM HEPES, PH 8 AND 0.9-1.1M AMSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.7→45 Å / Num. obs: 14997 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 13 % / Biso Wilson estimate: 100 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 33
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.2 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.7→45.18 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.904 / SU B: 11.501 / SU ML: 0.242 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.437 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.287 746 5.1 %RANDOM
Rwork0.246 ---
obs0.249 13915 97.8 %-
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: 73.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.04 Å20 Å2
2--0.07 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.7→45.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2101 0 25 29 2155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0212177
X-RAY DIFFRACTIONr_bond_other_d0.0020.021939
X-RAY DIFFRACTIONr_angle_refined_deg1.8231.9562963
X-RAY DIFFRACTIONr_angle_other_deg0.87234467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4695274
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_restr0.0820.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022458
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02486
X-RAY DIFFRACTIONr_nbd_refined0.2250.2444
X-RAY DIFFRACTIONr_nbd_other0.2210.22078
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0870.21265
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2340.237
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0010.21
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3470.214
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.931.51378
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.72822206
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6873799
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9354.5755
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: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.362 59
Rwork0.298 1010
Refinement TLS params.Method: refined / Origin x: 0 Å / Origin y: 0 Å / Origin z: 0 Å
111213212223313233
T0 Å20 Å20 Å2-0 Å20 Å2--0 Å2
L0 °20 °20 °2-0 °20 °2--0 °2
S0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °0 Å °

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