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- PDB-2vau: Isopenicillin N synthase with substrate analogue ACOMP (unexposed) -

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Basic information

Entry
Database: PDB / ID: 2vau
TitleIsopenicillin N synthase with substrate analogue ACOMP (unexposed)
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-V20 / Isopenicillin N synthase
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsGe, W. / Clifton, I.J. / Adlington, R.M. / Baldwin, J.E. / Rutledge, P.J.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: Isopenicillin N Synthase Mediates Thiolate Oxidation to Sulfenate in a Depsipeptide Substrate Analogue: Implications for Oxygen Binding and a Link to Nitrile Hydratase?
Authors: Ge, W. / Clifton, I.J. / Stok, J.E. / Adlington, R.M. / Baldwin, J.E. / Rutledge, P.J.
History
DepositionSep 4, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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 1.4May 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)38,0023
Polymers37,5641
Non-polymers4382
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.697, 71.161, 100.912
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-V20 / N6^-[(1R)-2-[(1S)-1-CARBOXY-2-(METHYLSULFANYL)ETHOXY]-2-OXO-1-(SULFANYLMETHYL)ETHYL]-6-OXO-L-LYSINE


Mass: 382.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H22N2O7S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O
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: 1.99 Å3/Da / Density % sol: 37.58 % / 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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 17, 2005 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→34.3 Å / Num. obs: 31926 / % possible obs: 98.4 % / Redundancy: 9 % / Biso Wilson estimate: 13.47 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 21
Reflection shellResolution: 1.79→1.89 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 7.2 / % possible all: 89

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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: 1.8→30.41 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.867 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ANISOTROPIC U FACTORS CALCULATED FROM TLS MODEL BY TLSANL.
RfactorNum. reflection% reflectionSelection details
Rfree0.19 1245 3.9 %RANDOM
Rwork0.151 ---
obs0.152 30604 99.8 %-
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: 5.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2645 0 25 345 3015
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222743
X-RAY DIFFRACTIONr_bond_other_d0.0020.021831
X-RAY DIFFRACTIONr_angle_refined_deg1.7221.953732
X-RAY DIFFRACTIONr_angle_other_deg2.23534460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4225328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82824.681141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5315428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.1331512
X-RAY DIFFRACTIONr_chiral_restr0.1140.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023091
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02561
X-RAY DIFFRACTIONr_nbd_refined0.2180.2541
X-RAY DIFFRACTIONr_nbd_other0.2210.21818
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21364
X-RAY DIFFRACTIONr_nbtor_other0.0860.21344
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2231
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2880.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.241.52102
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.44622668
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.78531314
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8614.51064
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: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.208 81
Rwork0.174 2184
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)
11.26450.0434-0.41011.6109-0.04491.9737-0.04170.03560.0119-0.01180.03060.05990.011-0.09770.01120.0333-0.0038-0.02040.04380.00220.03774.367933.4784-16.2796
20.3670.36960.69570.82551.16212.52310.0181-0.044-0.00610.0748-0.016-0.00230.1205-0.0441-0.00210.02260.0110.00080.0260.0010.03429.794625.312312.45
30.8046-0.2388-0.39030.49230.25250.634-0.0005-0.10170.02810.05470.0142-0.0460.01420.0557-0.01370.02760.0054-0.01110.0340.00060.024919.87328.803211.4538
40.29630.08570.16390.5125-0.16160.63050.00690.02690.0338-0.0157-0.0117-0.0204-0.02950.02260.00480.0343-0.0052-0.01280.02390.00430.044412.916932.2929-2.5983
50.6252-0.0478-0.12890.53490.09530.59610.0260.04760.0957-0.0651-0.0181-0.0109-0.09650.0054-0.0080.02760.0044-0.00530.00870.00330.02879.774842.1954-3.0036
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 46
2X-RAY DIFFRACTION2A47 - 79
3X-RAY DIFFRACTION3A80 - 143
4X-RAY DIFFRACTION4A144 - 201
5X-RAY DIFFRACTION5A202 - 331

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