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- PDB-1jx9: Penicillin Acylase, mutant -

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Basic information

Entry
Database: PDB / ID: 1jx9
TitlePenicillin Acylase, mutant
Components
  • penicillin G acylase alpha subunit
  • penicillin G acylase beta subunit
KeywordsHYDROLASE / Ntn-hydrolase fold / helices / beta-strands
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
Penicillin G acylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsHensgens, C.M.H. / Keizer, E. / Snijder, H.J. / Dijkstra, B.W.
CitationJournal: Protein Eng.Des.Sel. / Year: 2004
Title: Structural and kinetic studies on ligand binding in wild-type and active-site mutants of penicillin acylase.
Authors: Alkema, W.B. / Hensgens, C.M. / Snijder, H.J. / Keizer, E. / Dijkstra, B.W. / Janssen, D.B.
History
DepositionSep 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)86,2463
Polymers86,2062
Non-polymers401
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13940 Å2
ΔGint-100 kcal/mol
Surface area28070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.586, 63.965, 64.020
Angle α, β, γ (deg.)72.61, 74.09, 73.68
Int Tables number1
Space group name H-MP1
DetailsThe unit cell and asymetric unit contain the alpha and beta subunit of PA which together form the biological relevant structure

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Components

#1: Protein penicillin G acylase alpha subunit / penicillin G amidase / penicillin G amidohydrolase


Mass: 23838.822 Da / Num. of mol.: 1 / Fragment: alpha subunit of penicillin acylase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PAC / Plasmid: pEC / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P06875, penicillin amidase
#2: Protein penicillin G acylase beta subunit / penicillin G amidase / penicillin G amidohydrolase


Mass: 62367.426 Da / Num. of mol.: 1 / Fragment: beta subunit of penicillin acylase / Mutation: V148L, F24A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: PAC / Plasmid: pEC / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P06875, penicillin amidase
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.15 Å3/Da / Density % sol: 42.86 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: MOPS buffer, PEG MME 2k, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14-10 mg/mlprotein1drop
250 mMMOPS1droppH7.2
350 mMMOPS1reservoirpH7.2
412-20 %(w/v)PEG2000 MME1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAC Science DIP-2020 / Detector: IMAGE PLATE / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.28→30 Å / Num. all: 32764 / Num. obs: 31355 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 24.2 Å2 / Rsym value: 0.068 / Net I/σ(I): 9.6
Reflection shellResolution: 2.28→2.3 Å / Mean I/σ(I) obs: 3.9 / Rsym value: 0.163 / % possible all: 93.6
Reflection
*PLUS
Num. obs: 30372 / % possible obs: 95.1 % / Num. measured all: 193740 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 93.6 % / Rmerge(I) obs: 0.163

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Processing

Software
NameVersionClassification
REFMAC5refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PNK

1pnk


Resolution: 2.28→29.88 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.887 / SU B: 7.099 / SU ML: 0.179 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.502 / ESU R Free: 0.241 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22278 1612 5.1 %RANDOM
Rwork0.16581 ---
obs0.16873 29743 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 19.844 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.19 Å2-0.27 Å2
2--0.03 Å2-0.24 Å2
3---0.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.241 Å0.226 Å
Luzzati sigma a-0.179 Å
Refinement stepCycle: LAST / Resolution: 2.28→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6067 0 1 416 6484
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0216234
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.928491
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1463761
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.063151058
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0870.2897
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024869
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.33271
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.5680
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1120.53
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.354
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.58
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.5971.53798
X-RAY DIFFRACTIONr_mcangle_it1.12226114
X-RAY DIFFRACTIONr_scbond_it1.98232436
X-RAY DIFFRACTIONr_scangle_it3.1734.52377
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellHighest resolution: 2.28 Å / Rfactor Rfree: 0.222 / Rfactor Rwork: 0.176 / Total num. of bins used: 20
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.215 / Rfactor Rwork: 0.162
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.384
X-RAY DIFFRACTIONr_dihedral_angle_d
X-RAY DIFFRACTIONr_dihedral_angle_deg15.783

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