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- PDB-1w04: Isopenicillin N Synthase Aminoadipoyl-Cysteinyl-Glycine-Fe-NO Complex -

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Basic information

Entry
Database: PDB / ID: 1w04
TitleIsopenicillin N Synthase Aminoadipoyl-Cysteinyl-Glycine-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. / 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 ...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
: / DELTA-(L-ALPHA-AMINOADIPOYL)-L-CYSTEINYL-GLYCINE / HYDROXYAMINE / Isopenicillin N synthase
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 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

Downloads & links

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Assembly

Deposited unit
A: ISOPENICILLIN N SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1666
Polymers37,5641
Non-polymers6025
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.652, 70.752, 100.973
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, 332 molecules

#2: Chemical ChemComp-HCG / DELTA-(L-ALPHA-AMINOADIPOYL)-L-CYSTEINYL-GLYCINE


Mass: 321.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19N3O6S
#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.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1997
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.28→16.1 Å / Num. obs: 79915 / % possible obs: 92.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 10.8
Reflection shellResolution: 1.28→1.35 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 3.2 / % possible all: 85.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BK0
Resolution: 1.28→57.74 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.625 / SU ML: 0.027 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.175 3172 4 %RANDOM
Rwork0.162 ---
obs0.163 76679 92.2 %-
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: 7.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2--0.39 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.28→57.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2638 0 34 327 2999
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0212740
X-RAY DIFFRACTIONr_bond_other_d0.0030.022333
X-RAY DIFFRACTIONr_angle_refined_deg2.0021.9453727
X-RAY DIFFRACTIONr_angle_other_deg1.02635457
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6475328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1550.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.023082
X-RAY DIFFRACTIONr_gen_planes_other0.0170.02564
X-RAY DIFFRACTIONr_nbd_refined0.3370.2553
X-RAY DIFFRACTIONr_nbd_other0.2470.22722
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0880.21508
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2197
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2660.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1330.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2930.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9231.51646
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.45722654
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.38431094
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3294.51073
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: 1.28→1.31 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.321 204
Rwork0.309 4629
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)
111.3417-13.6731-8.256923.170515.166711.7618-0.06810.1707-0.0902-0.115-0.54090.9836-0.2929-0.81850.6090.11040.026-0.03790.1814-0.00850.1326-4.148837.4758-10.2071
26.65581.4002-2.7742.5134-1.94217.1205-0.31760.2871-0.2864-0.34970.0936-0.20130.64820.16050.22410.1403-0.03070.01960.1025-0.02760.074810.940324.8083-20.7825
33.7756-2.1335-1.45744.33771.48525.8855-0.08930.2603-0.0951-0.01350.00130.08730.1842-0.22520.0880.054-0.0167-0.00510.10390.02580.02897.473533.5642-21.5898
41.7433-0.3694-0.64564.168-0.77162.32880.03360.12620.1318-0.2431-0.01350.2552-0.1219-0.1477-0.02020.05870.0089-0.01770.09040.01440.04543.230436.4527-12.3019
51.2437-0.08050.97561.7953-1.12776.2342-0.0069-0.0482-0.0785-0.0175-0.0180.02450.08870.01140.02490.0357-0.0110.00140.02820.00240.05255.505419.6012-0.1539
63.62252.62127.31272.75995.476217.73480.1119-0.3032-0.15410.21270.00830.07140.1149-0.5636-0.12020.10430.00070.00990.0780.02170.06557.086922.838116.1977
75.56310.59471.12434.39190.65823.6473-0.03110.0489-0.03990.02720.0357-0.1251-0.01150.1591-0.00470.04590.003-0.00380.0705-0.01470.014116.696532.262819.8341
80.3121-0.2023-1.02661.8094-1.77815.8395-0.0184-0.21010.15650.1830.0239-0.119-0.26510.6265-0.00550.0608-0.0099-0.00460.1267-0.02660.071821.677334.381416.2604
95.2863-1.054-0.72391.03631.04153.0152-0.0735-0.41250.11520.0581-0.01060.0802-0.2593-0.13990.08410.08090.0155-0.01160.0837-0.01280.06126.631736.785118.7055
104.2939-0.4651-2.24910.81110.35261.344-0.0081-0.1995-0.01030.0370.001-0.09590.01110.08320.00710.03490.0053-0.01760.0260.00560.026721.749627.15796.3687
118.3784-3.64470.72576.62570.352.6474-0.0857-0.21930.2380.07570.1468-0.3128-0.0210.0849-0.06120.0301-0.0089-0.01060.0532-0.00660.053932.942232.43975.4476
123.51692.6931-1.28043.9121-1.07971.93110.1561-0.3577-0.13970.3515-0.1897-0.0010.07640.12950.03360.07080.0055-0.00250.07160.0130.054620.385422.839913.2896
130.3126-0.11140.86543.6643-3.47247.6820.0236-0.0584-0.13650.08290.03420.06370.2658-0.0848-0.05780.0435-0.00520.00550.03770.01330.062114.38818.29837.0855
140.9098-1.03081.30571.653-1.88724.2209-0.03510.1192-0.0662-0.09890.0383-0.02530.10040.0293-0.00320.0252-0.00540.00390.02940.00220.030715.553825.7136-6.3968
151.35580.8647-1.36392.1671-1.54338.0477-0.01720.07420.0387-0.0852-0.0839-0.1775-0.05050.27970.10110.0495-0.0169-0.01120.06710.02220.047716.297635.3178-18.5024
162.3353-2.33482.60033.1467-3.81735.64040.02280.33420.1203-0.171-0.1122-0.27530.0550.30760.08940.0684-0.00830.01180.09380.01970.064923.492631.9871-12.5337
177.4490.3199-3.09361.0824-0.17342.5646-0.0221-0.00060.01160.02710.00060.01260.0196-0.06840.02150.02180.002-0.01920.0115-0.00250.01713.016231.12355.3221
180.50460.89180.227710.21070.52593.0579-0.0319-0.17640.14910.5639-0.09120.2056-0.3282-0.26080.12310.12130.0035-0.01720.1132-0.0040.0885-4.28838.001818.1981
195.2279-2.2626-0.54258.1026-0.99292.3406-0.0455-0.2010.26520.37710.08030.1666-0.2642-0.0812-0.03480.08710.00630.00970.0493-0.00460.0917-2.024147.21368.4349
201.2423-0.4076-1.0260.78140.90942.4090.10820.03270.2116-0.0277-0.0181-0.0597-0.1923-0.0436-0.09020.03970.0019-0.00080.02660.01040.064810.827241.6728-1.8489
213.0657-1.5056-0.33171.3739-0.04140.1124-0.0241-0.0479-0.1130.1003-0.020.19330.0309-0.180.04420.0592-0.0113-0.00450.0961-0.00930.0557-0.739334.53420.5359
225.44165.8175-0.820325.00991.93183.6971-0.08130.16970.5772-1.2665-0.15111.0549-0.2486-0.32820.23240.10340.0489-0.04240.1420.01560.113-3.409544.3337-4.8236
232.08671.32880.23633.64620.55931.6199-0.0050.10980.08040.00060.06190.25170.0865-0.1638-0.0570.03760.0078-0.00660.05330.01020.04214.853332.8397-5.7835
242.51240.23460.58661.80050.86495.86750.20150.21490.3052-0.2233-0.0683-0.0067-0.3867-0.1704-0.13330.11680.00990.03710.05850.04270.08715.146745.6967-12.4358
252.18010.6585-2.1421.0232-1.2452.76640.08010.12790.12360.01330.0080.0589-0.1073-0.2036-0.08810.05350.00590.00060.0519-0.00060.0639-0.435441.86043.7263
265.91380.6298-3.70110.6727-0.42892.9087-0.02990.07680.07150.02390.01770.0550.0242-0.11950.01220.02620.0006-0.0160.0297-0.00210.03289.474631.96281.9441
274.3512-4.15465.23434.6989-6.715511.0390.1690.35010.1615-0.2768-0.2402-0.182-0.11660.41530.07120.1223-0.00230.0150.07890.00160.105624.56342.679-11.834
282.21540.87743.93341.8719-0.9297.3313-0.2320.49070.3306-0.5236-0.0564-0.1041-0.2750.190.28840.30620.01020.03620.19190.0210.180520.437951.5238-18.3616
294.1221-1.403-3.08523.43360.98566.72840.0651-0.16460.32890.25170.02-0.252-0.15510.3546-0.08510.0739-0.0125-0.0120.03680.00360.103723.035943.2295-0.4248
306.41710.4592-1.1373.9970.67553.30010.0865-0.1090.0690.08410.0715-0.0196-0.12270.0057-0.15790.1226-0.0038-0.01380.0663-0.00760.119213.621245.52369.2233
3111.9769-2.32612.77321.70741.838-2.9642-0.0488-0.6491-0.11880.05750.10460.2169-0.0891-0.1695-0.05590.07510.0120.02270.10920.00840.099911.63337.88515.2487
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 13
2X-RAY DIFFRACTION2A14 - 24
3X-RAY DIFFRACTION3A25 - 35
4X-RAY DIFFRACTION4A36 - 46
5X-RAY DIFFRACTION5A47 - 57
6X-RAY DIFFRACTION6A58 - 68
7X-RAY DIFFRACTION7A69 - 79
8X-RAY DIFFRACTION8A80 - 90
9X-RAY DIFFRACTION9A91 - 101
10X-RAY DIFFRACTION10A102 - 112
11X-RAY DIFFRACTION11A113 - 123
12X-RAY DIFFRACTION12A124 - 134
13X-RAY DIFFRACTION13A135 - 145
14X-RAY DIFFRACTION14A146 - 156
15X-RAY DIFFRACTION15A157 - 167
16X-RAY DIFFRACTION16A168 - 178
17X-RAY DIFFRACTION17A179 - 189
18X-RAY DIFFRACTION18A190 - 200
19X-RAY DIFFRACTION19A201 - 211
20X-RAY DIFFRACTION20A212 - 222
21X-RAY DIFFRACTION21A223 - 233
22X-RAY DIFFRACTION22A234 - 244
23X-RAY DIFFRACTION23A245 - 255
24X-RAY DIFFRACTION24A256 - 266
25X-RAY DIFFRACTION25A267 - 277
26X-RAY DIFFRACTION26A278 - 288
27X-RAY DIFFRACTION27A289 - 299
28X-RAY DIFFRACTION28A300 - 310
29X-RAY DIFFRACTION29A311 - 321
30X-RAY DIFFRACTION30A322 - 331
31X-RAY DIFFRACTION31A1332

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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