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- PDB-3zku: Isopenicillin N synthase with substrate analogue AhCV -

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Basic information

Entry
Database: PDB / ID: 3zku
TitleIsopenicillin N synthase with substrate analogue AhCV
ComponentsISOPENICILLIN N SYNTHASE
KeywordsOXIDOREDUCTASE / ANTIBIOTIC BIOSYNTHESIS / 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
: / Chem-HCV / Isopenicillin N synthase
Similarity search - Component
Biological speciesEMERICELLA NIDULANS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsDaruzzaman, A. / Clifton, I.J. / Rutledge, P.J.
CitationJournal: Chembiochem / Year: 2013
Title: The Interaction of Isopenicillin N Synthase with Homologated Substrate Analogues Delta-(L-Alpha-Aminoadipoyl)-L-Homocysteinyl-D-Xaa Characterised by Protein Crystallography.
Authors: Daruzzaman, A. / Clifton, I.J. / Adlington, R.M. / Baldwin, J.E. / Rutledge, P.J.
History
DepositionJan 24, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Database references
Revision 1.2Apr 10, 2013Group: Database references / Other
Revision 1.3Jul 5, 2017Group: Refinement description / Category: software
Revision 1.4Dec 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 / 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 / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)37,9973
Polymers37,5641
Non-polymers4332
Water4,630257
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.480, 71.105, 101.045
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 SYNTHETASE / IPNS


Mass: 37563.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) EMERICELLA NIDULANS (mold) / Plasmid: PJB703 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): NM554 / References: UniProt: P05326, isopenicillin-N synthase
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-HCV / N-[(5S)-5-amino-5-carboxypentanoyl]-L-homocysteyl-D-valine / Delta-L-alpha-aminoadipoyl-L-homocysteinyl-D-valine


Mass: 377.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H27N3O6S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.26 Å3/Da / Density % sol: 46 % / Description: NONE
Crystal growpH: 8.5
Details: 1.0M LITHIUM SULPHATE, 76MM TRIS/HCL PH 8.5, 2.0MM FERROUS SULPHATE, 2.6MG/ML SUBSTRATE, 25MG/ML IPNS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 27, 2002 / Details: MIRROR
RadiationMonochromator: DIAMOND (1 1 1) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.4→42 Å / Num. obs: 66426 / % possible obs: 99.4 % / Redundancy: 4.4 % / Biso Wilson estimate: 12.9 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.6
Reflection shellResolution: 1.4→1.43 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4.6 / % possible all: 89.1

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BK0
Resolution: 1.4→41.22 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.475 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1827 2646 4 %RANDOM
Rwork0.16125 ---
obs0.16212 63701 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.446 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.4 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.4→41.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2616 0 26 257 2899
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192782
X-RAY DIFFRACTIONr_bond_other_d0.0010.022553
X-RAY DIFFRACTIONr_angle_refined_deg2.0391.9443794
X-RAY DIFFRACTIONr_angle_other_deg1.01635887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4895336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.26324.577142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.03415432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6831512
X-RAY DIFFRACTIONr_chiral_restr0.1760.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213215
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02673
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.195 191 -
Rwork0.181 4261 -
obs--91.6 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
121.7277-11.4682-15.665617.196412.95925.12270.15350.3801-0.1469-0.3287-0.62690.7998-0.0742-1.35640.47340.0397-0.0012-0.06290.13830.00210.1408-8.41843.09-7.048
20.69180.3908-0.15440.5409-0.45581.3104-0.06260.1004-0.0032-0.05930.0326-0.0010.0813-0.09110.030.0484-0.0152-0.01130.05590.00930.03046.05131.398-16.827
31.12050.61123.12340.75581.81568.76480.0284-0.1678-0.01450.03560.0007-0.01810.0065-0.4478-0.02910.0651-0.0030.00410.07330.01810.03755.33520.7258.84
42.03461.1053-0.04371.05471.01622.66950.01030.0352-0.02480.05330.108-0.0337-0.0390.2295-0.11840.07310.01120.01250.0719-0.01120.03718.74532.75320.322
51.2062-0.2541-0.35080.3450.10040.4278-0.017-0.10570.05840.01920.0191-0.0478-0.02490.0207-0.00210.0392-0.0001-0.01710.0506-0.00240.054619.0331.50110.482
61.62121.2091-0.57371.2494-0.11540.78440.0201-0.13790.01060.0942-0.03340.00110.090.0820.01330.04810.0116-0.00560.04170.0130.057519.60423.30110.533
70.0663-0.09940.27430.6967-0.91031.962-0.02070.0368-0.0026-0.05810.0021-0.02310.04530.03790.01870.0473-0.01110.00230.0510.00560.044715.44229.146-10.443
82.0251-0.64333.77850.4071-1.36097.17730.04930.20820.0322-0.0916-0.1614-0.0880.16860.45520.11210.05460.00090.03890.10530.02310.048622.47933.88-16.38
93.4538-1.8164-0.31552.8221-0.11592.40250.01660.10890.1061-0.0484-0.037-0.17040.04790.14060.02040.02860.00490.00890.04570.00990.063225.36728.883-5.391
108.383-0.6022-5.32150.25970.30383.4130.10750.04510.07280.0496-0.03650.0422-0.0988-0.037-0.07110.0458-0.0020.00230.0842-0.01730.06556.23331.9659.436
110.69843.1682-0.907714.9813-3.16042.71220.10270.00560.01390.4822-0.0920.0578-0.2419-0.1885-0.01060.09220.0142-0.0250.0543-0.01820.0586-3.83241.51717.961
120.6588-0.2139-0.44290.66830.14610.29890.0601-0.03680.07210.012-0.0180.0443-0.04490.0229-0.04210.0411-0.0044-0.00110.0444-0.00430.06934.71542.9312.543
131.9550.0203-0.93711.4148-0.56650.6836-0.02150.0915-0.03950.0574-0.01730.0258-0.0026-0.06940.03880.026-0.02610.00090.0941-0.0430.0642-2.33937.6490.241
142.95761.31780.16339.3962-1.36630.31270.21480.13670.2637-0.3484-0.32070.53440.09580.00830.10590.03370.00680.02070.1274-0.09730.2127-3.8341.244-4.749
150.6235-0.0145-0.43530.3145-0.01180.57440.04450.02620.0645-0.0413-0.0350.0345-0.0666-0.0243-0.00950.037-0.004-0.00640.03920.0070.05746.97241.178-4.418
161.21140.0543-1.01810.1951-0.29621.4812-0.02810.03360.0953-0.0074-0.0236-0.0279-0.0806-0.04410.05170.05370.0113-0.02190.04290.0060.06816.19834.395-0.683
174.8541-1.2518.15872.932-4.136115.3691-0.20170.2239-0.01530.11230.2216-0.0282-0.50490.134-0.01990.1370.0360.0390.07260.03020.032919.26447.97-19.385
183.20451.74892.6531.61381.45762.1968-0.35970.3520.2013-0.13330.1526-0.1555-0.33540.29170.20710.1323-0.0599-0.01380.05890.05560.151723.74351.347-15.482
194.5353-0.5047-3.74394.23240.46993.32010.0517-0.26820.24380.2933-0.0037-0.1605-0.0970.253-0.0480.0502-0.0187-0.04140.03210.00430.119423.1443.360.233
2028.8122-21.0584-11.957715.39168.73994.9632-0.3121-0.73620.71170.24770.5691-0.51430.14710.3001-0.2570.2249-0.0841-0.02950.1113-0.06740.140614.93647.7698.068
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 8
2X-RAY DIFFRACTION2A9 - 49
3X-RAY DIFFRACTION3A50 - 66
4X-RAY DIFFRACTION4A67 - 86
5X-RAY DIFFRACTION5A87 - 119
6X-RAY DIFFRACTION6A120 - 143
7X-RAY DIFFRACTION7A144 - 166
8X-RAY DIFFRACTION8A167 - 174
9X-RAY DIFFRACTION9A175 - 180
10X-RAY DIFFRACTION10A181 - 192
11X-RAY DIFFRACTION11A193 - 201
12X-RAY DIFFRACTION12A202 - 224
13X-RAY DIFFRACTION13A225 - 234
14X-RAY DIFFRACTION14A235 - 246
15X-RAY DIFFRACTION15A247 - 278
16X-RAY DIFFRACTION16A279 - 293
17X-RAY DIFFRACTION17A294 - 302
18X-RAY DIFFRACTION18A303 - 311
19X-RAY DIFFRACTION19A312 - 321
20X-RAY DIFFRACTION20A322 - 327

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