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- PDB-2jb4: Isopenicillin N synthase with a 2-thiabicycloheptan-6-one product... -

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Basic information

Entry
Database: PDB / ID: 2jb4
TitleIsopenicillin N synthase with a 2-thiabicycloheptan-6-one product analogue
ComponentsIsopenicillin N synthase
KeywordsOXIDOREDUCTASE / ANTIBIOTIC BIOSYNTHESIS / PENICILLIN BIOSYNTHESIS / IRON / OXYGENASE / VITAMIN C / METAL-BINDING / 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-A14 / : / Isopenicillin N synthase
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsStewart, A.C. / Clifton, I.J. / Adlington, R.M. / Baldwin, J.E. / Rutledge, P.J.
Citation
Journal: Chembiochem / Year: 2007
Title: A Cyclobutanone Analogue Mimics Penicillin in Binding to Isopenicillin N Synthase.
Authors: Stewart, A.C. / Clifton, I.J. / Adlington, R.M. / Baldwin, J.E. / Rutledge, P.J.
#1: Journal: Nature / Year: 1999
Title: The Reaction Cycle of Isopenicillinn Synthase Observed by X-Ray Diffraction
Authors: Burzlaff, N.I. / Rutledge, P.J. / Clifton, I.J. / Hensgens, C.M.H. / Pickford, M. / Adlington, R.M. / Roach, P.L. / Baldwin, J.E.
History
DepositionDec 1, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2007Provider: 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: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code

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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)38,2626
Polymers37,5641
Non-polymers6985
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.677, 71.273, 100.906
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 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)
Gene: ipnA, ips, AN2622 / 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, 408 molecules

#2: Chemical ChemComp-A14 / (1S,4S,5S,7R)-7-{[(5S)-5-AMINO-5-CARBOXYPENTANOYL]AMINO}-3,3-DIMETHYL-6-OXO-2-THIABICYCLO[3.2.0]HEPTANE-4-CARBOXYLIC ACID


Mass: 358.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N2O6S
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: 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: 2.23 Å3/Da / Density % sol: 44.4 % / Description: NONE
Crystal growpH: 8.5
Details: 1.0M LITHIUM SULPHATE, 76MM TRIS/HCL, PH 8.5, 2.0MM FERROUS SULPHATE, 6.8 MM SUBSTRATE, 25MG/ML IPNS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 7, 2003 / Details: RH COATED TOROIDAL MIRRORS
RadiationMonochromator: GE (2 2 0) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.3→30.9 Å / Num. obs: 80123 / % possible obs: 96.3 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.8
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.1 / % possible all: 78.4

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Processing

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

1bk0


Resolution: 1.3→57.74 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.366 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.048 / 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
Rfree0.176 4023 5 %RANDOM
Rwork0.153 ---
obs0.154 76025 96.2 %-
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: 7.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--0.45 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.3→57.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2637 0 41 403 3081
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222767
X-RAY DIFFRACTIONr_bond_other_d0.0020.021830
X-RAY DIFFRACTIONr_angle_refined_deg1.821.9533765
X-RAY DIFFRACTIONr_angle_other_deg1.75834460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1685328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.26624.648142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.04115428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3141512
X-RAY DIFFRACTIONr_chiral_restr0.1320.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023099
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02566
X-RAY DIFFRACTIONr_nbd_refined0.2210.2516
X-RAY DIFFRACTIONr_nbd_other0.1940.21891
X-RAY DIFFRACTIONr_nbtor_refined0.1930.21381
X-RAY DIFFRACTIONr_nbtor_other0.090.21421
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.2276
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2590.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1720.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.231.51743
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6722669
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.84831252
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0094.51093
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
Rfree0.265 227
Rwork0.251 3918
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)
17.183-8.3218-4.802613.27477.41595.7866-0.0470.0949-0.0774-0.2144-0.21330.6201-0.2591-0.47120.2602-0.00180.0177-0.0490.0523-0.00030.0117-3.2836.811-11.012
21.12010.4108-0.39780.9749-0.59652.1202-0.08740.14480.0017-0.12320.0394-0.04340.0812-0.0910.0480.034-0.0103-0.01220.04230.0030.01046.9531.667-17.242
30.60290.55151.95541.12982.11056.50720.0633-0.1218-0.05860.14940.0008-0.01150.0919-0.2129-0.06410.0185-0.00840.00910.01590.0081-0.00016.42221.44411.051
42.69650.1898-0.11342.07271.40454.03420.03470.01380.09760.01040.0819-0.1115-0.11740.3756-0.11650.00890.0036-0.00450.0577-0.0135-0.006419.80234.11619.668
51.4521-0.2723-0.39980.6870.24390.9416-0.0017-0.12120.07530.05040.0176-0.0413-0.0240.0231-0.01590.02680.0044-0.02120.0303-0.00480.026718.84431.55810.512
61.95061.2521-0.36741.72510.09081.00040.0148-0.14550.01050.146-0.02370.00830.09750.05830.00890.03530.0185-0.00550.02960.00950.024119.64623.42210.324
70.1454-0.17810.40941.0462-1.28752.6235-0.04790.07130.0181-0.1093-0.0028-0.05730.05980.04530.05080.0227-0.0062-0.00160.02660.00950.014215.56929.241-10.467
80.8149-1.18781.70752.5236-2.30723.91170.0230.20320.0664-0.222-0.0847-0.08750.13270.30780.0617-0.0014-0.00580.00770.04270.014-0.003623.75631.963-12.606
96.0193-0.1998-4.03250.50640.06623.00930.0649-0.03510.04020.0624-0.05040.0609-0.071-0.0738-0.01440.0070.0045-0.01350.0316-0.01270.01937.43331.9548.562
102.86890.95910.565222.8239-2.22741.9474-0.0601-0.15190.19531.74580.01690.0078-0.469-0.37410.04320.14150.0208-0.02540.0341-0.0316-0.0017-4.65540.18619.238
110.9514-0.4242-0.76180.9670.50440.9790.034-0.03770.09310.0317-0.02440.0985-0.0735-0.0615-0.00960.01260.0064-0.0110.0218-0.00760.02593.60541.4252.768
124.10442.5899-1.17178.2077-1.36812.50870.03820.13160.2909-0.2948-0.08060.2762-0.0652-0.07040.0424-0.00680.037-0.0280.0406-0.0080.0311-3.16142.784-3.151
130.71780.0102-0.34390.51390.03670.61960.01750.01530.0635-0.0577-0.02260.0325-0.0548-0.03920.00510.01610.0033-0.01440.01870.00080.02447.50238.641-3.132
142.5945-2.06254.11593.5807-5.778510.7494-0.01810.20730.0915-0.01330.0075-0.0907-0.48570.15520.01060.06890.00110.02990.01630.02520.007722.55445.727-15.519
150.9067-0.2933-0.3951.27050.16841.5939-0.0039-0.14430.05950.1044-0.0195-0.0126-0.13580.08480.02340.0146-0.0164-0.0051-0.0211-0.00830.0419.59646.3480.276
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 14
2X-RAY DIFFRACTION2A15 - 49
3X-RAY DIFFRACTION3A50 - 69
4X-RAY DIFFRACTION4A70 - 86
5X-RAY DIFFRACTION5A87 - 119
6X-RAY DIFFRACTION6A120 - 143
7X-RAY DIFFRACTION7A144 - 166
8X-RAY DIFFRACTION8A167 - 179
9X-RAY DIFFRACTION9A180 - 192
10X-RAY DIFFRACTION10A193 - 199
11X-RAY DIFFRACTION11A200 - 227
12X-RAY DIFFRACTION12A228 - 244
13X-RAY DIFFRACTION13A245 - 288
14X-RAY DIFFRACTION14A289 - 304
15X-RAY DIFFRACTION15A305 - 331

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