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- PDB-1qje: Isopenicillin N synthase from Aspergillus nidulans (IP1 - Fe complex) -

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Basic information

Entry
Database: PDB / ID: 1qje
TitleIsopenicillin N synthase from Aspergillus nidulans (IP1 - Fe complex)
ComponentsISOPENICILLIN ...
KeywordsB-LACTAM ANTIBIOTIC / OXYGENASE / PENICILLIN BIOSYNTHESIS / ENZYME-PRODUCT COMPLEX
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
L-D-(A-AMINOADIPOYL)-L-CYSTEINYL-D-VALINE / : / ISOPENICILLIN N / Isopenicillin N synthase
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsBurzlaff, N.I. / Clifton, I.J. / Rutledge, P.J. / 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 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _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
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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 1.5May 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

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Assembly

Deposited unit
A: ISOPENICILLIN N SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4395
Polymers37,5641
Non-polymers8754
Water8,863492
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.670, 71.910, 101.730
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

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ISOPENICILLIN ... , 1 types, 1 molecules A

#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 (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (mold)
Gene: PCB C / Plasmid: PJB703 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): NM554 / References: UniProt: P05326

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Non-polymers , 5 types, 496 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-IP1 / ISOPENICILLIN N


Mass: 359.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H21N3O6S
#4: Chemical ChemComp-ACV / L-D-(A-AMINOADIPOYL)-L-CYSTEINYL-D-VALINE


Mass: 363.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H25N3O6S
#5: Chemical ChemComp-FE2 / FE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 492 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsIN THIS COMPLEX THE MOLECULES OF ISOPENICILLIN N (IP1) AND L-A-(D-AMINOADIPOYL)-L-CYSTEINYL-D- ...IN THIS COMPLEX THE MOLECULES OF ISOPENICILLIN N (IP1) AND L-A-(D-AMINOADIPOYL)-L-CYSTEINYL-D-VALINE (ACV) OCCUPY SIMILAR SITES AND ARE PRESENT IN A RATIO OF 7:3, WITH THE S ATOM OF ACV BOUND TO THE FE(II) ATOM.

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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: 37 %
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: Jun 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8345 Å / Relative weight: 1
ReflectionResolution: 1.35→25 Å / Num. obs: 69285 / % possible obs: 92.2 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.0078 / Net I/σ(I): 8.4
Reflection shellResolution: 1.35→1.37 Å / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 1.8 / % possible all: 43
Reflection
*PLUS
Num. measured all: 404650 / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 43 % / Num. unique obs: 1595 / Num. measured obs: 9310

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Processing

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

1bk0


Resolution: 1.35→25 Å / Num. restraintsaints: 34969 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1874 3421 5 %RANDOM
obs0.1309 -92.2 %-
all-65506 --
Refine analyzeNum. disordered residues: 3 / Occupancy sum hydrogen: 2516.4 / Occupancy sum non hydrogen: 3131.5
Refinement stepCycle: LAST / Resolution: 1.35→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2632 0 54 492 3178
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.043
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol0.067
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.069
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.012
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.306
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.036
X-RAY DIFFRACTIONs_approx_iso_adps0.094

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