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- PDB-2wo7: Isopenicillin N synthase with substrate analogue L,L,D-ACd2Ab (un... -

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Basic information

Entry
Database: PDB / ID: 2wo7
TitleIsopenicillin N synthase with substrate analogue L,L,D-ACd2Ab (unexposed)
ComponentsISOPENICILLIN N SYNTHASE
KeywordsOXIDOREDUCTASE / B-LACTAM ANTIBIOTIC / METAL-BINDING / MONOCYCLIC INTERMEDIATE / 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. / B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Isopenicillin N synthase, conserved site / Isopenicillin N synthase signature 2. / 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. / B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Isopenicillin N synthase, conserved site / Isopenicillin N synthase signature 2. / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGe, W. / Clifton, I.J. / Adlington, R.M. / Baldwin, J.E. / Rutledge, P.J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2010
Title: Crystallographic Studies on the Binding of Selectively Deuterated Lld- and Lll-Substrate Epimers by Isopenicillin N Synthase.
Authors: Ge, W. / Clifton, I.J. / Stok, J.E. / Adlington, R.M. / Baldwin, J.E. / Rutledge, P.J.
History
DepositionJul 22, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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 SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9673
Polymers37,5641
Non-polymers4032
Water5,477304
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.484, 75.935, 101.016
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 SYNTHASE / ISOPENICILLIN N SYNTHASE / IPNS


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-ASV / DELTA-(L-ALPHA-AMINOADIPOYL)-L-CYSTEINYL-D-VINYLGLYCINE


Mass: 347.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H21N3O6S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsD-L-A-AMINOADIPOYL-L-CYSTEINYL-D-2-AMINO-3, 3DIDEUTERIOBUTYRATE (ASV): DI-DEUTERATED ON BETA CARBON ...D-L-A-AMINOADIPOYL-L-CYSTEINYL-D-2-AMINO-3, 3DIDEUTERIOBUTYRATE (ASV): DI-DEUTERATED ON BETA CARBON OF AMINOBUTYRATE

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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: 2.13 Å3/Da / Density % sol: 42.41 % / 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: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 23, 2006 / Details: MIRRORS
RadiationMonochromator: SI (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.5→41.5 Å / Num. obs: 11384 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.21 / Net I/σ(I): 8.4
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.5 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0066refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BK0

1bk0


Resolution: 2.5→60.75 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.814 / SU B: 24.97 / SU ML: 0.257 / Cross valid method: THROUGHOUT / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ANISOTROPIC U VALUES FROM TLS MODEL. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25684 452 4 %RANDOM
Rwork0.18605 ---
obs0.18888 10905 97.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.091 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.92 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 2.5→60.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2631 0 24 304 2959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222728
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.9463714
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9065328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45724.71138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0815421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7011511
X-RAY DIFFRACTIONr_chiral_restr0.0830.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212155
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3951.51652
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.74222665
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.36231076
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1614.51049
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: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 30 -
Rwork0.208 803 -
obs--98.46 %
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)
10.5538-0.1164-0.36460.59650.19453.18170.0504-0.05830.05530.05890.0259-0.1272-0.14150.249-0.07630.0185-0.0126-0.01370.0408-0.00610.102214.98172.14974.7784
21.0550.17260.23131.08210.11882.0311-0.0061-0.01670.03480.01430.01250.0301-0.0773-0.0196-0.00630.00660.00120.00870.0121-0.00270.021710.5882-0.31582.3263
31.3618-0.64370.64372.41222.03146.10680.0462-0.1151-0.15170.09420.10710.14040.2556-0.5003-0.15340.0633-0.07480.03520.1601-0.00040.1597-3.9623-1.621-1.0925
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 114
2X-RAY DIFFRACTION2A115 - 298
3X-RAY DIFFRACTION3A299 - 331

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