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- PDB-1e3a: A slow processing precursor penicillin acylase from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 1e3a
TitleA slow processing precursor penicillin acylase from Escherichia coli
Components(PENICILLIN AMIDASE ...) x 2
KeywordsANTIBIOTIC RESISTANCE / AMIDASE / NTN-HYDROLASE / HYDROLYSIS OF PENICILLIN G ACYLASE
Function / homology
Function and homology information


penicillin amidase / penicillin amidase activity / antibiotic biosynthetic process / periplasmic space / response to antibiotic / metal ion binding
Similarity search - Function
Penicillin G acylase, C-terminal / Penicillin amidase (Acylase) alpha subunit, N-terminal domain / Aminohydrolase, alpha-helical knob region / Penicillin Amidohydrolase, domain 1 / Penicillin Amidohydrolase; domain 1 / Penicillin G acylase, beta-roll domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region / Penicillin/GL-7-ACA/AHL acylase / Penicillin/GL-7-ACA/AHL/aculeacin-A acylase / Penicillin amidase type, domain 1 ...Penicillin G acylase, C-terminal / Penicillin amidase (Acylase) alpha subunit, N-terminal domain / Aminohydrolase, alpha-helical knob region / Penicillin Amidohydrolase, domain 1 / Penicillin Amidohydrolase; domain 1 / Penicillin G acylase, beta-roll domain / Aminohydrolase, N-terminal nucleophile (Ntn) domain, beta-sheet knob region / Penicillin/GL-7-ACA/AHL acylase / 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 / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Penicillin G acylase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHewitt, L. / Kasche, V. / Lummer, K. / Lewis, R.J. / Murshudov, G.N. / Verma, C.S. / Dodson, G.G. / Wilson, K.S.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Structure of a Slow Processing Precursor Penicillin Acylase from Escherichia Coli Reveals the Linker Peptide Blocking the Active-Site Cleft
Authors: Hewitt, L. / Kasche, V. / Lummer, K. / Lewis, R.J. / Murshudov, G.N. / Verma, C.S. / Dodson, G.G. / Wilson, K.S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallisation of a Precursor Penicillin Acylase from Escherichia Coli
Authors: Hewitt, L. / Kasche, V. / Lummer, K. / Rieks, A. / Wilson, K.S.
History
DepositionJun 7, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.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: PENICILLIN AMIDASE ALPHA SUBUNIT
B: PENICILLIN AMIDASE BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9107
Polymers91,6482
Non-polymers2625
Water21,4921193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.710, 64.270, 72.000
Angle α, β, γ (deg.)66.14, 74.18, 74.23
Int Tables number1
Space group name H-MP1

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Components

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PENICILLIN AMIDASE ... , 2 types, 2 molecules AB

#1: Protein PENICILLIN AMIDASE ALPHA SUBUNIT / PGA


Mass: 28963.695 Da / Num. of mol.: 1 / Fragment: PENICILLIN AMIDASE RESIDUES 29-286
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: HB101 / Cellular location: PERIPLASM / Gene: PAC / Plasmid: PHM12 / Gene (production host): PAC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K5 / References: UniProt: P06875, penicillin amidase
#2: Protein PENICILLIN AMIDASE BETA SUBUNIT / PGA


Mass: 62684.770 Da / Num. of mol.: 1 / Fragment: PENICILLIN AMIDASE RESIDUES 287-846 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: HB101 / Cellular location: PERIPLASM / Gene: PAC / Plasmid: PHM12 / Gene (production host): PAC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K5 / References: UniProt: P06875, penicillin amidase

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Non-polymers , 4 types, 1198 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1193 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCHAIN B ENGINEERED MUTATION THR263GLY
Sequence detailsSWISS-PROT SEQ: SIGNAL REMOVED ON TRANSLOCATION TO PERIPLAS

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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: 2.17 Å3/Da / Density % sol: 43 %
Crystal growpH: 7.2
Details: 50MM MOPS PH7.2, 18-20% PEG 5KME, 10MM CACL2, pH 7.20
Crystal
*PLUS
Density % sol: 43 %
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop / pH: 7.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17.5 mg/mlprotein1drop
250 mMMOPS1reservoirpH7.2
318-22 %(v/v)PEG MME50001reservoir
410 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9096
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1997 / Details: SEGMENTED MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9096 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 70642 / % possible obs: 96.9 % / Redundancy: 1.9 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 10.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.216 / Mean I/σ(I) obs: 3.16 / % possible all: 89.1
Reflection
*PLUS
Num. measured all: 133678
Reflection shell
*PLUS
% possible obs: 89.1 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PNK

1pnk


Resolution: 1.8→20 Å / SU B: 2.5 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.12
RfactorNum. reflection% reflectionSelection details
Rfree0.197 3562 5 %RANDOM
Rwork0.158 ---
obs0.149 72879 96.9 %-
Displacement parametersBiso mean: 15.1 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6455 0 14 1193 7662
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.090.02
X-RAY DIFFRACTIONp_angle_d0.0260.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0290.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.152
X-RAY DIFFRACTIONp_mcangle_it1.673
X-RAY DIFFRACTIONp_scbond_it1.52
X-RAY DIFFRACTIONp_scangle_it2.23
X-RAY DIFFRACTIONp_plane_restr0.020.03
X-RAY DIFFRACTIONp_chiral_restr0.1130.15
X-RAY DIFFRACTIONp_singtor_nbd0.170.3
X-RAY DIFFRACTIONp_multtor_nbd0.2460.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1770.3
X-RAY DIFFRACTIONp_planar_tor47
X-RAY DIFFRACTIONp_staggered_tor13.615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor26.820
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_bond_d / Dev ideal: 0.009

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