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- PDB-2x1d: The crystal structure of mature acyl coenzyme A:isopenicillin N a... -

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Basic information

Entry
Database: PDB / ID: 2x1d
TitleThe crystal structure of mature acyl coenzyme A:isopenicillin N acyltransferase from Penicillium chrysogenum
ComponentsACYL-COENZYME
KeywordsTRANSFERASE / ZYMOGEN / NTN-HYDROLASE / PENICILLIN BIOSYNTHESIS / ANTIBIOTIC BIOSYNTHESIS
Function / homology
Function and homology information


isopenicillin-N N-acyltransferase / isopenicillin-N N-acyltransferase activity / penicillin biosynthetic process / peroxisomal matrix
Similarity search - Function
Arc Repressor Mutant, subunit A - #2120 / : / : / Peptidase C45 / Acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase / Penicillin V Acylase; Chain A / Penicillin V Acylase; Chain A / 4-Layer Sandwich / Arc Repressor Mutant, subunit A / Orthogonal Bundle ...Arc Repressor Mutant, subunit A - #2120 / : / : / Peptidase C45 / Acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase / Penicillin V Acylase; Chain A / Penicillin V Acylase; Chain A / 4-Layer Sandwich / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / (4S,5S)-1,2-DITHIANE-4,5-DIOL / PHOSPHATE ION / Isopenicillin-N N-acyltransferase
Similarity search - Component
Biological speciesPENICILLIUM CHRYSOGENUM (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsBokhove, M. / Yoshida, H. / Hensgens, C.M.H. / van der Laan, J.M. / Sutherland, J.D. / Dijkstra, B.W.
CitationJournal: Structure / Year: 2010
Title: Structures of an Isopenicillin N Converting Ntn-Hydrolase Reveal Different Catalytic Roles for the Active Site Residues of Precursor and Mature Enzyme.
Authors: Bokhove, M. / Yoshida, H. / Hensgens, C.M.H. / Van Der Laan, J.M. / Sutherland, J.D. / Dijkstra, B.W.
History
DepositionDec 23, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Refinement description / Version format compliance
Revision 1.2Nov 5, 2014Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Structure summary
Revision 1.3Dec 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_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACYL-COENZYME
B: ACYL-COENZYME
C: ACYL-COENZYME
D: ACYL-COENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,07218
Polymers160,0934
Non-polymers97914
Water16,376909
1
A: ACYL-COENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2464
Polymers40,0231
Non-polymers2233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ACYL-COENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2485
Polymers40,0231
Non-polymers2254
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ACYL-COENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1183
Polymers40,0231
Non-polymers942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ACYL-COENZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4606
Polymers40,0231
Non-polymers4375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)198.711, 68.219, 146.964
Angle α, β, γ (deg.)90.00, 128.64, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
ACYL-COENZYME / ISOPENICILLIN-N N-ACYLTRANSFERASE / ACYL-COENZYME A\:6-AMINOPENICILLANIC-ACID-ACYLTRANSFERASE 11 ...ISOPENICILLIN-N N-ACYLTRANSFERASE / ACYL-COENZYME A\:6-AMINOPENICILLANIC-ACID-ACYLTRANSFERASE 11 KDA SUBUNIT / ACYL-COENZYME A\:6-AMINOPENICILLANIC-ACID-ACYLTRANSFERASE 29 KDA SUBUNIT


Mass: 40023.234 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PENICILLIUM CHRYSOGENUM (fungus) / Strain: AS-P-78 / Plasmid: PKC787 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109
References: UniProt: P15802, isopenicillin-N N-acyltransferase

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Non-polymers , 6 types, 923 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-D1D / (4S,5S)-1,2-DITHIANE-4,5-DIOL


Mass: 152.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2S2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 909 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.4 % / Description: NONE
Crystal growpH: 7 / Details: 1.95 M NA/KPO4 BUFFER, PH 6.9, 25MM NAOAC

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.64→40 Å / Num. obs: 187993 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.7
Reflection shellResolution: 1.64→1.68 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.1 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X1C

2x1c


Resolution: 1.64→34.1 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.105 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20703 9288 5 %RANDOM
Rwork0.17944 ---
obs0.18083 175358 98.22 %-
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: 27.347 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0 Å2-0.06 Å2
2--0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.64→34.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11105 0 51 909 12065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02211663
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.95115790
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.54951467
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.44523.627579
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41151999
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.54815102
X-RAY DIFFRACTIONr_chiral_restr0.0880.21688
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219060
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.621.57180
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.143211528
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.00534483
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3954.54262
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: 1.64→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 720 -
Rwork0.248 12819 -
obs--98.17 %
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)
11.14620.0901-0.09821.23240.17570.97380.08020.04160.0067-0.0184-0.04320.0570.0029-0.0824-0.0370.02350.00590.00250.055-0.00410.0375-31.60634.2762.826
21.41010.1860.19750.66360.07990.9922-0.05750.09820.11580.02530.0127-0.0288-0.1011-0.01240.04480.04560.0080.00870.01070.01410.0295-46.4249.9436.388
31.37640.24990.21870.7560.26241.20710.0543-0.0178-0.1628-0.0121-0.0012-0.01830.14930.1381-0.05320.06740.03010.01310.02140.00530.0388-17.79823.66858.104
40.6960.02820.13551.1576-0.12481.3315-0.0070.01880.00050.04020.0205-0.03830.05670.1238-0.01350.03220.0208-0.00030.0434-0.01770.04725.9628.67726.881
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 355
2X-RAY DIFFRACTION2B1 - 356
3X-RAY DIFFRACTION3C1 - 356
4X-RAY DIFFRACTION4D1 - 355

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