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- PDB-1w06: Isopenicillin N Synthase Aminoadipoyl-Cysteinyl-Alanine-Fe NO Complex -

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Basic information

Entry
Database: PDB / ID: 1w06
TitleIsopenicillin N Synthase Aminoadipoyl-Cysteinyl-Alanine-Fe NO 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
: / HYDROXYAMINE / Chem-W05 / Isopenicillin N synthase
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLong, A.J. / Clifton, I.J. / Rutledge, P.J.
CitationJournal: Biochemistry / Year: 2005
Title: Structural Studies on the Reaction of Isopenicillin N Synthase with the Truncated Substrate Analogues Delta-(L-Alpha-Aminoadipoyl)-L-Cysteinyl-Glycine and Delta-(L-Alpha-Aminoadipoyl)-L-Cysteinyl-D- Alanine
Authors: Long, A.J. / Clifton, I.J. / Roach, P.L. / Baldwin, J.E. / Schofield, C.J. / Rutledge, P.J.
History
DepositionJun 1, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 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 1.3May 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)38,2767
Polymers37,5641
Non-polymers7126
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.130, 71.450, 101.880
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: 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)
Gene: PCB C / Plasmid: PJB703; OTHER_DETAILS: / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): NM554 / References: UniProt: P05326, isopenicillin-N synthase

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Non-polymers , 5 types, 345 molecules

#2: Chemical ChemComp-W05 / DELTA-(L-ALPHA-AMINOADIPOYL)-L-CYSTEINYL-D-ALANINE


Mass: 335.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H21N3O6S
#3: Chemical ChemComp-FE2 / FE (II) ION


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


Mass: 33.030 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H3NO
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCATALYTIC ACTIVITY: N-[(5S)-5-AMINO-5-CARBOXYPENTANOYL]-L- CYSTEINYL-D-VALINE + O2 => ISOPENICILLIN N + 2 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: 2.26 Å3/Da / Density % sol: 45 %
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: BM14 / Wavelength: 0.997
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 15, 1997 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 1.65→22 Å / Num. obs: 38692 / % possible obs: 92.3 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.115
Reflection shellResolution: 1.65→1.69 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.409 / % possible all: 85

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
Agrovatadata scaling
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BK0

1bk0


Resolution: 1.65→58.72 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.758 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1593 4.1 %RANDOM
Rwork0.17 ---
obs0.171 37099 91.7 %-
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: 10.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2--0.7 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.65→58.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2641 0 40 339 3020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0212751
X-RAY DIFFRACTIONr_bond_other_d0.0010.022343
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.7411.9473741
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg0.86935482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1160.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023086
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02563
X-RAY DIFFRACTIONr_nbd_refined0.2290.3490
X-RAY DIFFRACTIONr_nbd_other0.1950.32042
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0780.51
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.5224
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.36701
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2840.314
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2190.354
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.546
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9991.51648
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.64922657
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.68731103
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1474.51084
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: 1.65→1.69 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.258 102
Rwork0.21 2495
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)
10.7771-0.0776-0.05670.6482-0.00740.90280-0.00870.0526-0.00070.00350.0139-0.0487-0.0363-0.00350.0216-0.0033-0.0020.0012-0.00510.040411.766935.0694-0.1012
2-14.84343.60390.27484.48550.38252.43090.0826-0.58190.7822-0.0883-0.12680.14860.1614-0.31630.04420.04930.02140.00230.09510.01660.133311.056138.16514.9439
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 331
2X-RAY DIFFRACTION2A1332

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