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- PDB-2vcm: Isopenicillin N synthase with substrate analogue AsMCOV -

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Basic information

Entry
Database: PDB / ID: 2vcm
TitleIsopenicillin N synthase with substrate analogue AsMCOV
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 / 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 / Isopenicillin N synthase
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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
DepositionSep 25, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 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 / 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 SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1905
Polymers37,5641
Non-polymers6264
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.576, 75.353, 101.511
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-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
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.14 Å3/Da / Density % sol: 42.43 % / 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: PX10.1 / Wavelength: 1.075
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 23, 2005 / Details: RH MIRROR
RadiationMonochromator: SI (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.65→50.77 Å / Num. obs: 38350 / % possible obs: 97.7 % / Redundancy: 7.4 % / Biso Wilson estimate: 19.01 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 16
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.6 / % possible all: 85.1

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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: 1.65→60.52 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.576 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.097 / 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
Rfree0.203 1490 3.9 %RANDOM
Rwork0.166 ---
obs0.167 36795 97.6 %-
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: 10.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2--0.2 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.65→60.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2645 0 36 274 2955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222756
X-RAY DIFFRACTIONr_bond_other_d0.0010.021832
X-RAY DIFFRACTIONr_angle_refined_deg1.9221.9543754
X-RAY DIFFRACTIONr_angle_other_deg0.98634465
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3885330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00424.681141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.79815429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1871512
X-RAY DIFFRACTIONr_chiral_restr0.1250.2394
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023098
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02562
X-RAY DIFFRACTIONr_nbd_refined0.2170.2570
X-RAY DIFFRACTIONr_nbd_other0.1970.21958
X-RAY DIFFRACTIONr_nbtor_refined0.1910.21378
X-RAY DIFFRACTIONr_nbtor_other0.0950.21359
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2197
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1290.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2810.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4341.52097
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.71222674
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.18931316
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.334.51079
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
Rfree0.356 97
Rwork0.285 2203
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)
114.9241-5.24525.308452.7591-16.862529.31640.53880.3074-0.6488-0.6262-0.27870.53410.6130.628-0.260.09520.0368-0.0380.0529-0.07310.011716.748-20.489-4.386
21.24040.04730.42241.27520.00072.7018-0.00780.1280.0894-0.03110.0068-0.0649-0.11590.15610.00110.0851-0.00820.01640.09940.0038-0.002516.352-0.064-16.983
33.85491.84571.27443.25880.49742.1572-0.0632-0.05990.02760.0555-0.0139-0.1586-0.04640.09470.07710.09790.011-0.00670.1123-0.00720.033420.043-1.636-4.577
44.53850.2391-1.94370.29790.76656.14090.1416-0.0957-0.21090.00340.0953-0.1558-0.14950.6961-0.23690.0583-0.0205-0.02260.0975-0.0491-0.018720.5265.56319.823
50.15460.185-0.07861.1614-0.8752.5469-0.0014-0.07760.05920.0470.0302-0.0014-0.1568-0.1448-0.02880.1090.00640.00010.0923-0.019-0.01428.745.53717.476
67.7054-0.58361.8450.395-0.24552.29-0.0264-0.30790.33250.0480.0001-0.0167-0.4593-0.09780.02630.18020.00690.01360.0368-0.0553-0.01439.98115.72112.859
70.3741-0.03050.20890.13540.35972.91370.01030.05930.113-0.02520.01530.0327-0.3183-0.0006-0.02560.1301-0.01080.00820.07640.01350.016210.3539.178-6.562
83.8813-2.7023.15763.9697-3.24274.07760.1336-0.1998-0.11990.0213-0.058-0.07150.18050.0752-0.07560.09410.0117-0.0010.0845-0.0081-0.030917.463-3.74513.748
94.58874.38164.20576.52575.678310.87160.2682-0.3198-0.1620.4675-0.18150.19250.7213-0.2531-0.08670.1365-0.0151-0.00180.04290.028-0.0311.917-18.63415.514
100.7642-0.03510.15320.6957-0.23590.8509-0.02110.0239-0.07030.05150.0427-0.02820.03470.0053-0.02160.07910.0060.00390.0742-0.01260.001811.41-8.20.87
111.0320.40920.08830.66561.0363.9820.05210.1589-0.0354-0.1115-0.11920.0774-0.0465-0.68620.06710.05370.0419-0.02740.1511-0.0134-0.034-5.1922.084-9.609
121.0807-2.05631.87984.7673-2.67944.7886-0.0765-0.2742-0.09180.28610.19320.21150.1382-0.3594-0.11670.0631-0.00460.0360.1130.0045-0.0398-0.635-2.099.431
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 8
2X-RAY DIFFRACTION2A9 - 36
3X-RAY DIFFRACTION3A37 - 55
4X-RAY DIFFRACTION4A56 - 74
5X-RAY DIFFRACTION5A75 - 112
6X-RAY DIFFRACTION6A113 - 139
7X-RAY DIFFRACTION7A140 - 180
8X-RAY DIFFRACTION8A181 - 194
9X-RAY DIFFRACTION9A195 - 208
10X-RAY DIFFRACTION10A209 - 285
11X-RAY DIFFRACTION11A286 - 314
12X-RAY DIFFRACTION12A315 - 331

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