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- PDB-1ajp: PENICILLIN ACYLASE COMPLEXED WITH 2,5-DIHYDROXYPHENYLACETIC ACID -

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Basic information

Entry
Database: PDB / ID: 1ajp
TitlePENICILLIN ACYLASE COMPLEXED WITH 2,5-DIHYDROXYPHENYLACETIC ACID
Components(PENICILLIN AMIDOHYDROLASE) x 2
KeywordsANTIBIOTIC RESISTANCE / LIGAND INDUCED CONFORMATIONAL CHANGE / HYDROLASE
Function / homology
Function and homology information


penicillin amidase activity / penicillin amidase / antibiotic biosynthetic process / periplasmic space / response to antibiotic / metal ion binding
Similarity search - Function
Helix Hairpins - #150 / Penicillin G acylase, C-terminal / Penicillin Amidohydrolase, domain 1 / Penicillin Amidohydrolase; domain 1 / Penicillin amidase (Acylase) alpha subunit, N-terminal domain / Aminohydrolase, alpha-helical knob region / Penicillin/GL-7-ACA/AHL acylase / Penicillin G acylase, beta-roll domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region / Penicillin/GL-7-ACA/AHL/aculeacin-A acylase ...Helix Hairpins - #150 / Penicillin G acylase, C-terminal / Penicillin Amidohydrolase, domain 1 / Penicillin Amidohydrolase; domain 1 / Penicillin amidase (Acylase) alpha subunit, N-terminal domain / Aminohydrolase, alpha-helical knob region / Penicillin/GL-7-ACA/AHL acylase / Penicillin G acylase, beta-roll domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region / Penicillin/GL-7-ACA/AHL/aculeacin-A acylase / Penicillin amidase type, domain 1 / Penicillin amidase type, N-terminal domain, B-knob / Penicillin amidase type, A-knob / Penicillin amidase / Aminohydrolase, N-terminal nucleophile (Ntn) domain / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Helix Hairpins / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2-(3,6-DIHYDROXYPHENYL)ACETIC ACID / Penicillin G acylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS TO NATIVE / Resolution: 2.31 Å
AuthorsDone, S.H.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Ligand-induced conformational change in penicillin acylase.
Authors: Done, S.H. / Brannigan, J.A. / Moody, P.C.E. / Hubbard, R.E.
#2: Journal: Nature / Year: 1995
Title: Penicillin acylase has a single-amino-acid catalytic centre.
Authors: Duggleby, H.J. / Tolley, S.P. / Hill, C.P. / Dodson, E.J. / Dodson, G. / Moody, P.C.
#3: Journal: Protein Eng. / Year: 1990
Title: Expression, purification and crystallization of penicillin G acylase from Escherichia coli ATCC 11105.
Authors: Hunt, P.D. / Tolley, S.P. / Ward, R.J. / Hill, C.P. / Dodson, G.G.
#1: Journal: Structural Studies of Penicillin Acylase / Year: 1996
Authors: Done, S.H.
History
DepositionMay 7, 1997Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 12, 2012Group: Non-polymer description
Revision 1.4Jun 5, 2024Group: 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 / diffrn_source / pdbx_database_status / pdbx_struct_conn_angle / software / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _software.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_distant_solvent_atoms / pdbx_entry_details ...pdbx_distant_solvent_atoms / pdbx_entry_details / struct_conn / struct_conn_type
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PENICILLIN AMIDOHYDROLASE
B: PENICILLIN AMIDOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4764
Polymers86,2672
Non-polymers2082
Water11,926662
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14500 Å2
ΔGint-103 kcal/mol
Surface area28840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.120, 65.080, 76.300
Angle α, β, γ (deg.)100.20, 111.44, 105.81
Int Tables number1
Space group name H-MP1

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Components

#1: Protein PENICILLIN AMIDOHYDROLASE / PENICILLIN ACYLASE


Mass: 23838.824 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P06875, penicillin amidase
#2: Protein PENICILLIN AMIDOHYDROLASE / PENICILLIN ACYLASE


Mass: 62428.512 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P06875, penicillin amidase
#3: Chemical ChemComp-OMD / 2-(3,6-DIHYDROXYPHENYL)ACETIC ACID / HOMOGENTISIC ACID


Mass: 168.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 662 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN
Nonpolymer detailsTHERE IS DISORDER IN THE LIGAND WHICH IS ONLY 50% OCCUPIED.

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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: 3.06 Å3/Da / Density % sol: 59.5 %
Crystal growMethod: streak seeded / pH: 7.2
Details: CRYSTALLIZED FROM 10% PEG 8000, 50MM MOPS, PH 7.2, STREAK SEEDED. SOAKED IN 10MM 2,5-DIHYDROXYPHENYLACETIC ACID, streak seeded
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlpenicillin acylase1drop
225 mMMOPS1drop
35 %PEG80001drop
450 mMMOPS1reservoir
59-14 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.31→26.81 Å / Num. obs: 33820 / % possible obs: 96.1 % / Redundancy: 2 % / Biso Wilson estimate: 19.46 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 7.2
Reflection shellResolution: 2.31→2.44 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.179 / Mean I/σ(I) obs: 3.7 / % possible all: 84.7
Reflection
*PLUS
Num. measured all: 67021

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Processing

Software
NameVersionClassification
REFMACrefinement
DENZOdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: ISOMORPHOUS TO NATIVE / Resolution: 2.31→26.81 Å / Cross valid method: FREE R
Details: ISOMORPHOUS TO NATIVE THERE IS DISORDER IN A 145 AND A 146, BOTH HAVING DUAL CONFORMATIONS AS A RESULT OF LIGAND BINDING.
RfactorNum. reflection% reflectionSelection details
Rfree0.2252 2367 7 %BASED ON NATIVE
Rwork0.146 ---
obs-33820 96.1 %-
Displacement parametersBiso mean: 30.45 Å2
Refinement stepCycle: LAST / Resolution: 2.31→26.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6071 0 13 662 6746
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0370.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.040.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.8183
X-RAY DIFFRACTIONp_mcangle_it4.0275
X-RAY DIFFRACTIONp_scbond_it6.4185
X-RAY DIFFRACTIONp_scangle_it8.49710
X-RAY DIFFRACTIONp_plane_restr0.02450.03
X-RAY DIFFRACTIONp_chiral_restr0.1340.15
X-RAY DIFFRACTIONp_singtor_nbd0.1780.3
X-RAY DIFFRACTIONp_multtor_nbd0.3120.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1590.3
X-RAY DIFFRACTIONp_planar_tor4.97
X-RAY DIFFRACTIONp_staggered_tor19.615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor26.220
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.146
Solvent computation
*PLUS
Displacement parameters
*PLUS

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