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- PDB-1k5s: PENICILLIN ACYLASE, MUTANT COMPLEXED WITH PPA -

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Basic information

Entry
Database: PDB / ID: 1k5s
TitlePENICILLIN ACYLASE, MUTANT COMPLEXED WITH PPA
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 / 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
R-2-PHENYL-PROPRIONIC ACID / Penicillin G acylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.43 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.L. / Hensgens, C.M.H. / Snijder, H.J. / Keizer, E. / Dijkstra, B.W. / Janssen, D.B.
History
DepositionOct 12, 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 1.3Oct 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 1.4Aug 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)86,3974
Polymers86,2062
Non-polymers1902
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14590 Å2
ΔGint-94 kcal/mol
Surface area28210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.820, 64.360, 64.750
Angle α, β, γ (deg.)72.89, 74.01, 73.55
Int Tables number1
Space group name H-MP1
DetailsThe alpha and beta unit together form the biological unit / the alpha and beta unit together form the biological relevant unit

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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
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 / Mutation: F24A, V148L
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: Chemical ChemComp-GRO / R-2-PHENYL-PROPRIONIC ACID


Mass: 150.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H10O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 360 / 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: 2.11 Å3/Da / Density % sol: 41.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: MOPS BUFFER, PEG MME 2K, PPA, pH 7.20, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.2 / 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 / Wavelength: 1.5418 Å
DetectorType: MAC Science DIP-2020 / Detector: IMAGE PLATE / Date: Jan 1, 2000 / 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: 2.43→30 Å / Num. all: 27684 / Num. obs: 26632 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 2.185 % / Rsym value: 0.037 / Net I/σ(I): 21.1
Reflection shellResolution: 2.43→2.47 Å / Mean I/σ(I) obs: 10.9 / Rsym value: 0.066 / % possible all: 95.7
Reflection
*PLUS
Highest resolution: 2.43 Å / Lowest resolution: 30 Å / Num. measured all: 58181 / Rmerge(I) obs: 0.037
Reflection shell
*PLUS
% possible obs: 95.7 % / Rmerge(I) obs: 0.066 / Mean I/σ(I) obs: 10.9

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Processing

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

1pnk


Resolution: 2.43→30 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: engh & huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1375 5.2 %RANDOM
Rwork0.173 ---
obs0.194 26632 96.2 %-
Displacement parametersBiso mean: 18.104 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20.06 Å2-0.23 Å2
2--0.14 Å2-0.36 Å2
3---0.6 Å2
Refine analyzeLuzzati sigma a obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 2.43→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6067 0 12 360 6439
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d1.131
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord0.215
X-RAY DIFFRACTIONp_mcbond_it0.629
X-RAY DIFFRACTIONp_mcangle_it1.049
X-RAY DIFFRACTIONp_scbond_it1.569
X-RAY DIFFRACTIONp_scangle_it2.261
X-RAY DIFFRACTIONp_plane_restr0.004
X-RAY DIFFRACTIONp_chiral_restr0.075
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.139
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
LS refinement shellHighest resolution: 2.43 Å / Rfactor Rfree: 0.269 / Rfactor Rwork: 0.173 / Total num. of bins used: 20
Software
*PLUS
Version: 5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.131
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg16.787

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