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- PDB-2ve1: Isopenicillin N synthase with substrate analogue AsMCOV (oxygen e... -

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Basic information

Entry
Database: PDB / ID: 2ve1
TitleIsopenicillin N synthase with substrate analogue AsMCOV (oxygen exposed 1min 20bar)
ComponentsISOPENICILLIN N SYNTHETASE
KeywordsOXIDOREDUCTASE / ANTIBIOTIC BIOSYNTHESIS / PENICILLIN BIOSYNTHESIS / IRON / OXYGENASE / VITAMIN C / METAL-BINDING / MONOCYCLIC INTERMEDIATE / B-LACTAM ANTIBIOTIC
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-M11 / Chem-W2X / Isopenicillin N synthase
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGe, W. / Clifton, I.J. / Adlington, R.M. / Baldwin, J.E. / Rutledge, P.J.
CitationJournal: Chembiochem / Year: 2009
Title: Structural Studies on the Reaction of Isopenicillin N Synthase with a Sterically Demanding Depsipeptide Substrate Analogue.
Authors: Ge, W. / Clifton, I.J. / Howard-Jones, A.R. / Stok, J.E. / Adlington, R.M. / Baldwin, J.E. / Rutledge, P.J.
History
DepositionOct 15, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 2.0Jun 14, 2017Group: Atomic model / Derived calculations
Category: atom_site / pdbx_struct_conn_angle ...atom_site / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / struct_conf / struct_conn / struct_conn_type / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_seq_id / _atom_site.label_alt_id / _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.ptnr2_auth_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 / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.sheet_id / _struct_conf.pdbx_PDB_helix_id / _struct_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.sheet_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 2.2May 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)38,3914
Polymers37,5641
Non-polymers8273
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.672, 75.717, 101.910
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 SYNTHETASE / IPNS / 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, isopenicillin-N synthase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-W2X / N~6~-[(1R)-1-({[(1R,2R)-1-CARBOXY-3-HYDROXY-2-METHYLPROPYL]OXY}CARBONYL)-2-MERCAPTOPROP-2-EN-1-YL]-6-OXO-L-LYSINE


Mass: 392.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O8S
#4: Chemical ChemComp-M11 / N^6^-[(1R,2S)-1-({[(1R)-1-carboxy-2-methylpropyl]oxy}carbonyl)-2-sulfanylpropyl]-6-oxo-L-lysine


Mass: 378.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26N2O7S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsD-L-A-AMINOADIPOYL-(3S-METHYL)-L-CYSTEINE D-A-HYDROXYL ISOVALERYL ESTER (M11): SAME, EXCEPT FOR ...D-L-A-AMINOADIPOYL-(3S-METHYL)-L-CYSTEINE D-A-HYDROXYL ISOVALERYL ESTER (M11): SAME, EXCEPT FOR NUMBERING, AS LIGAND MDZ FROM DEPOSITION 2VCM
Sequence detailsRESIDUES 1-2 NOT SEEN

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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: 2.16 Å3/Da / Density % sol: 43.06 % / Description: NONE
Crystal growpH: 8.5
Details: 1.0M LITHIUM SULPHATE, 76MM TRIS/HCL, PH 8.5, 2.0MM FERROUS SULPHATE, 2.6MG/ML TRIPEPTIDE, 25MG/ML IPNS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: May 10, 2005 / Details: MIRRORS
RadiationMonochromator: SI (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→60.75 Å / Num. obs: 16731 / % possible obs: 98.5 % / Redundancy: 5.9 % / Biso Wilson estimate: 19.98 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 11.4
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.8 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BK0

1bk0


Resolution: 2.2→60.75 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.885 / SU B: 11.7 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.314 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ANISOTROPIC U FACTORS CALCULATED BY TLSANL FROM REFMAC TLS MODEL
RfactorNum. reflection% reflectionSelection details
Rfree0.246 649 3.9 %RANDOM
Rwork0.175 ---
obs0.178 16043 98.2 %-
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: 4.88 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20 Å2
2--0.27 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.2→60.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2645 0 52 168 2865
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222788
X-RAY DIFFRACTIONr_bond_other_d0.0020.021855
X-RAY DIFFRACTIONr_angle_refined_deg1.7291.963799
X-RAY DIFFRACTIONr_angle_other_deg2.2893.0014506
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6265334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75924.755143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95815433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1591512
X-RAY DIFFRACTIONr_chiral_restr0.0990.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023141
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02565
X-RAY DIFFRACTIONr_nbd_refined0.2180.2559
X-RAY DIFFRACTIONr_nbd_other0.220.21771
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21295
X-RAY DIFFRACTIONr_nbtor_other0.0910.21365
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2127
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2690.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0021.52131
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0622693
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.16331352
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9444.51103
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
Rfree0.282 30
Rwork0.201 1085
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)
11.0589-0.19790.52840.6649-0.52921.93180.00360.0437-0.1158-0.07260.027-0.0360.07060.155-0.03060.01020.00420.0160.0561-0.017-0.008416.954-3.595-12.801
26.6757-3.1186-15.58622.06514.117252.84860.3373-1.12850.539-0.00680.824-0.61170.05252.8257-1.1613-0.1778-0.0087-0.11610.3043-0.26770.207426.1994.6639.455
30.15020.3697-0.27161.0259-0.1712.6216-0.0031-0.0841-0.01550.10060.0548-0.0618-0.2853-0.0468-0.05170.02660.00360.00010.0141-0.00190.002810.5546.6318.587
40.5553-0.01150.30180.31950.14261.7468-0.0154-0.01850.01120.01590.03750.0008-0.22940.047-0.02210.0383-0.01390.0080.0196-0.0011-0.005811.9257.7973.96
50.52380.0680.29660.9205-0.29151.30610.0075-0.0368-0.08330.06190.0401-0.00540.0796-0.017-0.04760.01090.00660.0030.018-0.01360.000711.18-8.7161.786
60.6959-0.31780.61451.669-0.04775.7022-0.0006-0.0378-0.06360.143-0.02220.09270.0884-0.45550.0229-0.05680.00170.02480.0689-0.01610.0078-4.0910.117-2.845
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 50
2X-RAY DIFFRACTION2A51 - 62
3X-RAY DIFFRACTION3A63 - 114
4X-RAY DIFFRACTION4A115 - 198
5X-RAY DIFFRACTION5A199 - 289
6X-RAY DIFFRACTION6A290 - 331

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