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- PDB-1ips: ISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (MANGANESE COMPLEX) -

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Basic information

Entry
Database: PDB / ID: 1ips
TitleISOPENICILLIN N SYNTHASE FROM ASPERGILLUS NIDULANS (MANGANESE COMPLEX)
ComponentsISOPENICILLIN N SYNTHASE
KeywordsANTIBIOTIC BIOSYNTHESIS / B-LACTAM ANTIBIOTIC / OXYGENASE / PENICILLIN BIOSYNTHESIS / OXIDOREDUCTASE
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
: / Isopenicillin N synthase
Similarity search - Component
Biological speciesEmericella nidulans (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsRoach, P.L. / Clifton, I.J. / Fulop, V. / Harlos, K. / Barton, G.J. / Hajdu, J. / Andersson, I. / Schofield, C.J. / Baldwin, J.E.
Citation
Journal: Nature / Year: 1995
Title: Crystal structure of isopenicillin N synthase is the first from a new structural family of enzymes.
Authors: Roach, P.L. / Clifton, I.J. / Fulop, V. / Harlos, K. / Barton, G.J. / Hajdu, J. / Andersson, I. / Schofield, C.J. / Baldwin, J.E.
#1: Journal: Protein Sci. / Year: 1995
Title: Crystallization and Preliminary X-Ray Diffraction Studies on Recombinant Isopenicillin N Synthase from Aspergillus Nidulans
Authors: Roach, P.L. / Schofield, C.J. / Baldwin, J.E. / Clifton, I.J. / Hajdu, J.
History
DepositionMar 21, 1997Processing site: BNL
Revision 1.0Mar 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ISOPENICILLIN N SYNTHASE
B: ISOPENICILLIN N SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3476
Polymers75,1282
Non-polymers2204
Water3,495194
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.200, 127.000, 139.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (-0.74664, -0.60828, -0.26932), (-0.598, 0.43636, 0.6723), (-0.29142, 0.66302, -0.68955)
Vector: 73.39649, 37.23963, -18.37032)

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Components

#1: Protein ISOPENICILLIN N SYNTHASE


Mass: 37563.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (mold) / Gene: PCB C / Plasmid: PJB703 / Production host: Escherichia coli (E. coli) / Strain (production host): NM554 / References: UniProt: P05326
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 4

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Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.2 %
Crystal growMethod: microseeding / pH: 8.5
Details: CRYSTALS FROM MICROSEEDING USING 24% PEG 8000, 5MM MNCL2, 100MM TRIS/HCL, PH 8.5, microseeding
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Details: used to seeding, Roach, P.L., (1995) Protein Sci., 4, 1007.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
124 %PEG80001drop
25 mM1dropMnCl2
3100 mMTris-HCl1drop
4100 mMTris-HCl1reservoir
516 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.893
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Sep 1, 1994 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.893 Å / Relative weight: 1
ReflectionResolution: 2.5→24.5 Å / Num. obs: 36775 / % possible obs: 98.6 % / Redundancy: 2.3 % / Biso Wilson estimate: 53.3 Å2 / Rmerge(I) obs: 0.125 / Net I/σ(I): 17.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 6.8 / % possible all: 96.7
Reflection
*PLUS
Num. measured all: 136252

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Processing

Software
NameVersionClassification
DMmodel building
MLPHAREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: MIR / Resolution: 2.5→8 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: NCS RESTRAINTS: 200 (ENERGY-LIKE TERM), SIGB 1.5
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1449 4 %RANDOM
Rwork0.22 ---
obs0.22 36720 98.1 %-
Displacement parametersBiso mean: 38.5 Å2
Refine analyzeLuzzati sigma a obs: 0.45 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5277 0 4 194 5475
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.5→2.54 Å / Rfactor Rfree error: 0.07 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.488 50 3.4 %
Rwork0.359 1452 -
obs--85.8 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARHCSDX.PRO
X-RAY DIFFRACTION2PARAM.MN
X-RAY DIFFRACTION3PARAM11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.215 / Rfactor obs: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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