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- PDB-1qjf: ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (Monocyclic Su... -

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Basic information

Entry
Database: PDB / ID: 1qjf
TitleISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (Monocyclic Sulfoxide - Fe COMPLEX)
ComponentsISOPENICILLIN N SYNTHASE
KeywordsB-LACTAM ANTIBIOTIC / MONOCYCLIC INTERMEDIATE / OXYGENASE / PENICILLIN BIOSYNTHESIS / SULFOXIDE
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-ACS / : / Isopenicillin N synthase
Similarity search - Component
Biological speciesEMERICELLA NIDULANS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsRutledge, P.J. / Clifton, I.J. / Burzlaff, N.I. / Roach, P.L. / Adlington, R.M. / Baldwin, J.E.
Citation
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.
#1: 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.
#2: 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.
#3: Journal: Protein Sci. / Year: 1995
Title: Crystallization and Preliminary X-Ray Diffraction Studies on Recombinant Isopenicillin N Synthase from Aspergillus Nidulans
Authors: Roach, P.L. / Schofield, C.J. / Baldwin, J.E. / Clifton, I.J. / Hajdu, J.
History
DepositionJun 23, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 29, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 24, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.gene_src_strain
Revision 1.4Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Dec 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ISOPENICILLIN N SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1114
Polymers37,5641
Non-polymers5473
Water7,386410
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.777, 71.186, 101.251
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBIOLOGICAL_UNIT: MONOMER

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Components

#1: Protein ISOPENICILLIN N SYNTHASE /


Mass: 37563.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) EMERICELLA NIDULANS (mold) / Gene: PCB C / Plasmid: PJB703 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): NM554 / References: UniProt: P05326
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACS / 1-[(1S)-CARBOXY-2-(METHYLSULFINYL)ETHYL]-(3R)-[(5S)-5-AMINO-5-CARBOXYPENTANAMIDO]-(4R)-SULFANYLAZETIDIN-2-ONE


Mass: 395.452 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H21N3O7S2
#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 / Water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.226 Å3/Da / Density % sol: 38 %
Crystal growpH: 8.5
Details: 1.8M LITHIUM SULPHATE, 100MM TRIS/HCL (PH8.5) (5MM FERROUS SULPHATE, 70 MM ACMC, 50MG/ML IPNS), pH 8.50
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion, hanging drop
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: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8345
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8345 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 55209 / % possible obs: 85.3 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 3.6
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.2 / % possible all: 50.6
Reflection
*PLUS
Num. measured all: 344241
Reflection shell
*PLUS
% possible obs: 50.6 % / Num. unique obs: 4482 / Num. measured obs: 6601

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXLphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BK0

1bk0


Resolution: 1.4→8 Å / Num. restraintsaints: 33425 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: FINAL MAP GENERATED WITH CCP4
RfactorNum. reflection% reflectionSelection details
Rfree0.2047 2758 5 %RANDOM
obs0.1312 -85.3 %-
all-52208 --
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 2541 / Occupancy sum non hydrogen: 3059
Refinement stepCycle: LAST / Resolution: 1.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2639 0 31 410 3080
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.019
X-RAY DIFFRACTIONs_angle_d0.042
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.352
X-RAY DIFFRACTIONs_zero_chiral_vol0.049
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.053
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.058
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps

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