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- PDB-1oc1: ISOPENICILLIN N SYNTHASE aminoadipoyl-cysteinyl-aminobutyrate-FE ... -

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Basic information

Entry
Database: PDB / ID: 1oc1
TitleISOPENICILLIN N SYNTHASE aminoadipoyl-cysteinyl-aminobutyrate-FE COMPLEX
ComponentsISOPENICILLIN N SYNTHETASE
KeywordsOXIDOREDUCTASE / 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-ASV / : / Isopenicillin N synthase
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLong, A.J. / Clifton, I.J. / Roach, P.L. / Baldwin, J.E. / Schofield, C.J. / Rutledge, P.J.
Citation
Journal: Biochem.J. / Year: 2003
Title: Structural Studies on the Reaction of Isopenicillin N Synthase with the Substrate Analogue Delta-(L-Alpha-Aminoadipoyl)-L-Cysteinyl-D-Alpha-Aminobutyrate
Authors: Long, A.J. / Clifton, I.J. / Roach, P.L. / Baldwin, J.E. / Schofield, C.J. / Rutledge, P.J.
#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.
History
DepositionFeb 3, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 5, 2017Group: Refinement description / Category: software
Revision 1.3Oct 24, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.gene_src_strain
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_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 1.5May 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

Downloads & links

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Assembly

Deposited unit
A: ISOPENICILLIN N SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2556
Polymers37,5641
Non-polymers6915
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)100.976, 100.976, 115.658
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2123-

HOH

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Components

#1: Protein ISOPENICILLIN N SYNTHETASE / 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)
Plasmid: PJB703 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): NM554 / References: UniProt: P05326
#2: Chemical ChemComp-ASV / DELTA-(L-ALPHA-AMINOADIPOYL)-L-CYSTEINYL-D-VINYLGLYCINE


Mass: 347.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H21N3O6S
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 4.57 Å3/Da / Density % sol: 72.88 %
Crystal growpH: 8.5 / Details: pH 8.50
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: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→19 Å / Num. obs: 34696 / % possible obs: 99.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.7
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.3 / % possible all: 99.6
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 19 Å / Num. measured all: 124191 / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
% possible obs: 99.1 % / Num. unique obs: 5079 / Num. measured obs: 16871 / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.3

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Processing

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

1blz


Resolution: 2.2→87.71 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.756 / SU ML: 0.093 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1398 4 %RANDOM
Rwork0.173 ---
obs0.174 33292 98.8 %-
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: 13.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0.04 Å20 Å2
2---0.08 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.2→87.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2641 0 39 203 2883
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0212751
X-RAY DIFFRACTIONr_bond_other_d0.0020.022343
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.9473745
X-RAY DIFFRACTIONr_angle_other_deg1.20135481
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7655328
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_restr0.1030.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023090
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02563
X-RAY DIFFRACTIONr_nbd_refined0.210.2520
X-RAY DIFFRACTIONr_nbd_other0.2410.22673
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0880.21518
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2151
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1250.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3370.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7721.51647
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.39722659
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.45231104
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9294.51086
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: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.289 90
Rwork0.234 2489
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.7291-1.1849-0.17845.4751-1.13241.21250.0182-0.0664-0.09510.12470.06050.4853-0.0409-0.3189-0.07870.10370.05930.0260.07240.02840.125324.824728.483722.2029
22.4037-2.07690.71413.9535-1.06172.72590.08310.2171-0.1714-0.1982-0.0952-0.05780.21850.00390.01210.17080.07680.00110.0474-0.03140.078943.81476.683114.2672
31.9329-1.2567-0.00693.7870.60651.32890.25640.4214-0.0623-0.5461-0.2527-0.05490.1133-0.003-0.00370.17230.0844-0.01230.11390.02640.043236.461219.91467.7339
40.773-0.4942-0.04092.2694-0.73431.64460.05830.04110.08230.0357-0.1804-0.19880.00980.14850.1220.07220.0217-0.00370.0350.01390.084539.839718.748823.1068
51.4976-0.56790.05664.7875-2.35162.8571-0.0896-0.13190.10630.40090.02840.0901-0.2513-0.15910.06120.14230.0671-0.01140.04340.00340.046635.531424.172228.9143
62.66311.35020.02144.5221-0.9191.77-0.0069-0.01480.21520.3853-0.1952-0.7488-0.13480.57460.20210.21850.046-0.02150.19070.0260.204844.848529.586518.0894
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 57
2X-RAY DIFFRACTION2A58 - 112
3X-RAY DIFFRACTION3A113 - 167
4X-RAY DIFFRACTION4A168 - 222
5X-RAY DIFFRACTION5A223 - 277
6X-RAY DIFFRACTION6A278 - 331
Refinement
*PLUS
% reflection Rfree: 4 % / Rfactor Rfree: 0.199 / Rfactor Rwork: 0.171
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.03
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.4

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