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- PDB-1gm7: Crystal structures of penicillin acylase enzyme-substrate complex... -

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Basic information

Entry
Database: PDB / ID: 1gm7
TitleCrystal structures of penicillin acylase enzyme-substrate complexes: Structural insights into the catalytic mechanism
Components(PENICILLIN G ACYLASE ...) x 2
KeywordsHYDROLASE / ANTIBIOTIC RESISTANCE
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
Helix Hairpins - #150 / 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 ...Helix Hairpins - #150 / 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 / Helix Hairpins / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PENICILLIN G / Penicillin G acylase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.45 Å
AuthorsMcVey, C.E. / Walsh, M.A. / Dodson, G.G. / Wilson, K.S. / Brannigan, J.A.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Crystal Structures of Penicillin Acylase Enzyme- Substrate Complexes: Structural Insights Into the Catalytic Mechanism
Authors: Mcvey, C.E. / Walsh, M.A. / Dodson, G.G. / Wilson, K.S. / Brannigan, J.A.
#1: Journal: Protein Eng. / Year: 1990
Title: Expression, Purification and Crystallisation 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.
#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.E.
History
DepositionSep 11, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2001Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Dec 7, 2016Group: Database references
Revision 1.3Jul 24, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms ...diffrn_source / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PENICILLIN G ACYLASE ALPHA SUBUNIT
B: PENICILLIN G ACYLASE BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,85724
Polymers86,2412
Non-polymers1,61622
Water16,754930
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16710 Å2
ΔGint-123.5 kcal/mol
Surface area34540 Å2
MethodPQS
Unit cell
Length a, b, c (Å)51.600, 131.800, 63.900
Angle α, β, γ (deg.)90.00, 105.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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PENICILLIN G ACYLASE ... , 2 types, 2 molecules AB

#1: Protein PENICILLIN G ACYLASE ALPHA SUBUNIT / NTN / PENICILLIN AMIDOHYDROLASE


Mass: 23854.824 Da / Num. of mol.: 1 / Fragment: RESIDUES 27-235
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Cellular location: PERIPLASM / Gene: PAC / Plasmid: PACYC184PAC / Cellular location (production host): PERIPLASM / Gene (production host): PAC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06875, penicillin amidase
#2: Protein PENICILLIN G ACYLASE BETA SUBUNIT / NTN / PENICILLIN AMIDOHYDROLASE


Mass: 62386.473 Da / Num. of mol.: 1 / Fragment: RESIDUES 290-846 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Cellular location: PERIPLASM / Gene: PAC / Plasmid: PACYC184PAC / Cellular location (production host): PERIPLASM / Gene (production host): PAC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06875, penicillin amidase

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Non-polymers , 4 types, 952 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PNN / PENICILLIN G / Benzylpenicillin


Mass: 334.390 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18N2O4S / Comment: antibiotic*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 930 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 42.7 %
Crystal growpH: 7.5 / Details: pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.89
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. obs: 144035 / % possible obs: 99.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 18.7
Reflection shellResolution: 1.45→1.47 Å / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 3.3 / % possible all: 99.9

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.45→30 Å / SU B: 0.96 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.058
RfactorNum. reflection% reflectionSelection details
Rfree0.173 4323 3 %RANDOM
Rwork0.145 ---
obs-139473 99.6 %-
Displacement parametersBiso mean: 14.8 Å2
Refinement stepCycle: LAST / Resolution: 1.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6075 0 104 930 7109
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0190.02
X-RAY DIFFRACTIONp_angle_d0.0340.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0410.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.6473
X-RAY DIFFRACTIONp_mcangle_it2.1395
X-RAY DIFFRACTIONp_scbond_it3.7357
X-RAY DIFFRACTIONp_scangle_it4.96410
X-RAY DIFFRACTIONp_plane_restr0.02670.03
X-RAY DIFFRACTIONp_chiral_restr0.1390.15
X-RAY DIFFRACTIONp_singtor_nbd0.1620.3
X-RAY DIFFRACTIONp_multtor_nbd0.2630.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1490.3
X-RAY DIFFRACTIONp_planar_tor4.77
X-RAY DIFFRACTIONp_staggered_tor13.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.120
X-RAY DIFFRACTIONp_special_tor15

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