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- PDB-2bjs: Isopenicillin N synthase C-terminal truncation mutant -

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Basic information

Entry
Database: PDB / ID: 2bjs
TitleIsopenicillin N synthase C-terminal truncation mutant
ComponentsISOPENICILLIN N SYNTHETASE
KeywordsOXIDOREDUCTASE / ANTIBIOTIC BIOSYNTHESIS / B-LACTAM ANTIBIOTIC / IRON / OXYGENASE / PENICILLIN BIOSYNTHESIS / VITAMIN C
Function / homology
Function and homology information


isopenicillin-N synthase / isopenicillin-N synthase activity / penicillin biosynthetic process / 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 / : / METHANETHIOL / Isopenicillin N synthase
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsMcNeill, L.A. / Sami, M. / Clifton, I.J. / Burzlaff, N.I.
CitationJournal: Chemistry / Year: 2017
Title: Terminally Truncated Isopenicillin N Synthase Generates a Dithioester Product: Evidence for a Thioaldehyde Intermediate during Catalysis and a New Mode of Reaction for Non-Heme Iron Oxidases.
Authors: McNeill, L.A. / Brown, T.J.N. / Sami, M. / Clifton, I.J. / Burzlaff, N.I. / Claridge, T.D.W. / Adlington, R.M. / Baldwin, J.E. / Rutledge, P.J. / Schofield, C.J.
History
DepositionFeb 7, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Feb 21, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
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

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Assembly

Deposited unit
A: ISOPENICILLIN N SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8476
Polymers36,9201
Non-polymers9275
Water9,836546
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)47.149, 71.126, 100.991
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ISOPENICILLIN N SYNTHETASE / IPNS / ISOPENICILLIN N SYNTHASE


Mass: 36920.168 Da / Num. of mol.: 1 / Mutation: YES
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)
Description: ASPERGILLUS NIDULANS / Plasmid: PJB703 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): NM554 / References: UniProt: P05326, isopenicillin-N synthase

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Non-polymers , 5 types, 551 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-ACV / L-D-(A-AMINOADIPOYL)-L-CYSTEINYL-D-VALINE


Mass: 363.430 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H25N3O6S
#4: Chemical ChemComp-MEE / METHANETHIOL


Mass: 48.107 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4S
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsFUNCTION: REMOVES, IN THE PRESENCE OF OXYGEN, 4 HYDROGEN ATOMS FROM DELTA-L-(ALPHA-AMINOADIPYL)-L- ...FUNCTION: REMOVES, IN THE PRESENCE OF OXYGEN, 4 HYDROGEN ATOMS FROM DELTA-L-(ALPHA-AMINOADIPYL)-L-CYSTEINYL-D- VALINE (ACV) TO FORM THE AZETIDINONE AND THIAZOLIDINE RINGS OF ISOPENICILLIN
Sequence detailsRESIDUES 326-331 DELETED

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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: 2.32 Å3/Da / Density % sol: 46.47 %
Crystal growpH: 8.5
Details: 1.0M LITHIUM SULPHATE, 76MM TRIS/HCL (PH8.5), pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.93487
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 3, 1998 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93487 Å / Relative weight: 1
ReflectionResolution: 1.3→34.46 Å / Num. obs: 82674 / % possible obs: 98.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.6
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.3 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BK0

1bk0


Resolution: 1.3→58.12 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU ML: 0.025 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.164 3297 4 %RANDOM
Rwork0.139 ---
obs0.14 79248 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.3→58.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2571 0 49 546 3166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0222698
X-RAY DIFFRACTIONr_bond_other_d0.0010.022310
X-RAY DIFFRACTIONr_angle_refined_deg2.2461.9413675
X-RAY DIFFRACTIONr_angle_other_deg1.07835398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5115319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40924.604139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.90615410
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4151512
X-RAY DIFFRACTIONr_chiral_restr0.1380.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023038
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02560
X-RAY DIFFRACTIONr_nbd_refined0.2370.2508
X-RAY DIFFRACTIONr_nbd_other0.1840.22294
X-RAY DIFFRACTIONr_nbtor_refined0.1890.21340
X-RAY DIFFRACTIONr_nbtor_other0.090.21461
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2250.2331
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1040.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2410.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2620.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3041.51639
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.88822591
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.92731211
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2624.51084
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: 1.3→1.33 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.235 229
Rwork0.208 5512
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)
10.40460.2835-0.15610.8384-0.95341.7474-0.06090.0650.025-0.07170.0380.01630.0285-0.11850.0229-0.1122-0.0049-0.0131-0.1041-0.0013-0.12174.60930.703-12.85
20.3124-0.1514-0.43630.47860.47021.45730.0042-0.14960.03330.08290.00640.00170.02670.0481-0.0106-0.11420.0065-0.0122-0.0996-0.0072-0.126614.63630.7515.512
30.5443-0.00350.07360.62210.12240.6233-0.0131-0.02570.00490.03550.0204-0.04150.0430.057-0.0073-0.13730.007-0.0009-0.1298-0.0033-0.13120.07727.0710.252
40.81680.0904-0.02020.6039-0.13330.55970.0259-0.05510.1330.0306-0.01670.0484-0.0791-0.0152-0.0092-0.1189-0.0013-0.0147-0.1282-0.0115-0.11469.01437.8552.856
51.0376-0.0266-0.51490.55370.11870.94090.04190.03760.1117-0.0527-0.04110.0992-0.0998-0.0961-0.0008-0.10650.0136-0.0188-0.1029-0.0043-0.10263.54240.472-3.822
60.99370.0876-0.36160.8165-0.07631.11160.0610.07680.1906-0.0932-0.0388-0.1099-0.22620.0851-0.0222-0.069-0.00050.0006-0.10380.0158-0.076519.48742.36-6.676
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 - 322

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