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- PDB-1odn: ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (OXYGEN-EXPOSE... -

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Basic information

Entry
Database: PDB / ID: 1odn
TitleISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (OXYGEN-EXPOSED PRODUCT FROM ANAEROBIC AC-VINYLGLYCINE FE COMPLEX)
ComponentsISOPENICILLIN N SYNTHASE
KeywordsOXIDOREDUCTASE / ANTIBIOTIC BIOSYNTHESIS / B-LACTAM ANTIBIOTIC / OXYGENASE / PENICILLIN BIOSYNTHESIS
Function / homology
Function and homology information


isopenicillin-N synthase / isopenicillin-N synthase activity / penicillin biosynthetic process / L-ascorbic acid binding / iron ion binding / cytosol
Similarity search - Function
Isopenicillin N synthase signature 1. / Isopenicillin N synthase, conserved site / Isopenicillin N synthase signature 2. / B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Non-haem dioxygenase N-terminal domain / 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 ...Isopenicillin N synthase signature 1. / Isopenicillin N synthase, conserved site / Isopenicillin N synthase signature 2. / B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Non-haem dioxygenase N-terminal domain / 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-APV / : / Isopenicillin N synthase
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsElkins, J.M. / Rutledge, P.J. / Burzlaff, N.I. / Clifton, I.J. / Adlington, R.M. / Roach, P.L. / Baldwin, J.E.
Citation
Journal: Org.Biomol.Chem. / Year: 2003
Title: Crystallographic Studies on the Reaction of Isopenicillin N Synthase with an Unsaturated Substrate Analogue
Authors: Elkins, J.M. / Rutledge, P.J. / Burzlaff, N.I. / Clifton, I.J. / Adlington, R.M. / Roach, P.L. / Baldwin, J.E.
#1: Journal: Nature / Year: 1999
Title: The Reaction Cycle of Isopenicillin N Synthase Observed by X-Ray Diffraction
Authors: Burzlaff, N.I. / Rutledge, P.J. / Clifton, I.J. / Hensgens, C.M.H. / Pickford, M. / Adlington, R.M. / Roach, P.L. / Baldwin, J.E.
#2: Journal: Nature / Year: 1997
Title: Structure of Isopenicillin N Synthase Complexed with Substrate and the Mechanism of Penicillin Formation
Authors: Roach, P.L. / Clifton, I.J. / Hensgens, C.M. / Shibata, N. / Schofield, C.J. / Hajdu, J. / Baldwin, J.E.
#3: Journal: Nature / Year: 1995
Title: Crystal Structure of Isopenicillin N Synthase is the First from a New Structural Family of Enzymes
Authors: Roach, P.L. / Clifton, I.J. / Fulop, V. / Harlos, K. / Barton, G.J. / Hajdu, J. / Andersson, I. / Schofield, C.J. / Baldwin, J.E.
History
DepositionFeb 19, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 5, 2017Group: Refinement description / Category: software
Revision 1.3Dec 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
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
Revision 1.4May 8, 2024Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ISOPENICILLIN N SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0774
Polymers37,5641
Non-polymers5133
Water7,116395
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.742, 70.966, 101.010
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 ISOPENICILLIN N SYNTHASE / ISOPENICILLIN N SYNTHASE / IPNS


Mass: 37563.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (mold)
Plasmid: PJB703 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): NM554 / References: UniProt: P05326
#2: Chemical ChemComp-APV / 6-(5-AMINO-5-CARBOXY-PENTANOYLAMINO)-3-HYDROXYMETHYL-7-OXO-4-THIA-1-AZA-BICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID / ALPHA-HYDROXYMETHYL-BETA-DEMETHYL-ISOPENICILLIN N


Mass: 361.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N3O7S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-FE2 / FE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 395 / 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: 40 %
Crystal growpH: 7.5
Details: 1.8M LITHIUM SULPHATE, 100MM TRIS/HCL (PH8.5), (5MM FERROUS SULPHATE, 70 MM ACVG, 50MG/ML IPNS), pH 7.50
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop / Details: Roach, P.L., (1996) Eur. J. Biochem., 242, 736.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.8 Mlithium sulfate1reservoir
2100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 0.9312
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 4, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9312 Å / Relative weight: 1
ReflectionResolution: 1.6→41.17 Å / Num. obs: 42669 / % possible obs: 95.2 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 6.4
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 1.9 / % possible all: 94.2
Reflection
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 41.17 Å / Redundancy: 2.4 % / Num. measured all: 101990 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 94.2 % / Redundancy: 2.4 % / Num. unique obs: 6077 / Num. measured obs: 14387 / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QJE

1qje


Resolution: 1.6→38 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.359 / SU ML: 0.048 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.178 1683 3.9 %RANDOM
Rwork0.151 ---
obs0.153 40955 94.5 %-
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: 11.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2--0.86 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.6→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2583 0 30 395 3008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212687
X-RAY DIFFRACTIONr_bond_other_d0.0020.022284
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.9463663
X-RAY DIFFRACTIONr_angle_other_deg0.83935315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3285320
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_restr0.0950.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023022
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02553
X-RAY DIFFRACTIONr_nbd_refined0.2080.2514
X-RAY DIFFRACTIONr_nbd_other0.2450.22688
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.21481
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2249
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1110.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2580.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2260.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8651.51607
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.54722596
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.61931080
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2394.51067
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: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.268 120
Rwork0.235 2931
Refinement TLS params.Method: refined / Origin x: 11.664 Å / Origin y: 34.622 Å / Origin z: -0.432 Å
111213212223313233
T0.0546 Å20.0013 Å2-0.0051 Å2-0.0019 Å2-0.0027 Å2--0.0145 Å2
L0.5013 °20.0054 °2-0.0803 °2-0.4892 °20.0172 °2--0.5952 °2
S-0.0073 Å °-0.0102 Å °0.0782 Å °-0.0065 Å °-0.0043 Å °0.007 Å °-0.0359 Å °-0.0174 Å °0.0116 Å °
Refinement
*PLUS
Lowest resolution: 41.17 Å / % reflection Rfree: 4 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.48

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