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- PDB-1k5q: PENICILLIN ACYLASE, MUTANT COMPLEXED WITH PAA -

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Basic information

Entry
Database: PDB / ID: 1k5q
TitlePENICILLIN ACYLASE, MUTANT COMPLEXED WITH PAA
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
2-PHENYLACETIC ACID / Penicillin G acylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.34 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 1.3Jul 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
Revision 1.6Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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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)86,3824
Polymers86,2062
Non-polymers1762
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14510 Å2
ΔGint-94 kcal/mol
Surface area27760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.760, 63.960, 64.240
Angle α, β, γ (deg.)72.86, 73.91, 73.50
Int Tables number1
Space group name H-MP1
Detailsbeta and alpha subunit together give the biological assembly

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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: YES
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 / Fragment: phenyl acetic acid / Source method: obtained synthetically / Formula: Ca / Details: YES
#4: Chemical ChemComp-PAC / 2-PHENYLACETIC ACID


Mass: 136.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: MOPS BUFFER, PEG MME 2K, PAA , 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: 2.34→30 Å / Num. all: 30551 / Num. obs: 28382 / % possible obs: 92.9 % / Observed criterion σ(I): -3 / Redundancy: 1.943 % / Rsym value: 0.043 / Net I/σ(I): 15.9
Reflection shellResolution: 2.34→2.38 Å / Mean I/σ(I) obs: 5.5 / Rsym value: 0.098 / % possible all: 77.5
Reflection
*PLUS
Highest resolution: 2.34 Å / Lowest resolution: 19 Å / Num. measured all: 55158 / Rmerge(I) obs: 0.043
Reflection shell
*PLUS
% possible obs: 77.5 % / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 5.5

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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: 2.34→19.03 Å / SU ML: 0.272 / Cross valid method: THROUGHOUT / ESU R: 0.92 / Stereochemistry target values: engh&huber / Details: see remarks
RfactorNum. reflection% reflectionSelection details
Rfree0.21837 1461 5.2 %RANDOM
Rwork0.16337 ---
obs0.16616 26894 92.9 %-
all-28355 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 16.395 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20.53 Å2-0.54 Å2
2--0.1 Å2-0.53 Å2
3---1.04 Å2
Refine analyzeLuzzati sigma a obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.34→19.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6067 0 11 358 6436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d
X-RAY DIFFRACTIONr_bond_other_d0.0010.025404
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg0.87312599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0533761
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.076151061
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021289
X-RAY DIFFRACTIONr_nbd_refined0.2180.31518
X-RAY DIFFRACTIONr_nbd_other0.210.35742
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.318
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1910.338
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.59
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.57
X-RAY DIFFRACTIONr_mcangle_it1.089
X-RAY DIFFRACTIONr_scbond_it1.628
X-RAY DIFFRACTIONr_scangle_it2.734
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellHighest resolution: 2.34 Å / Rfactor Rfree: 0.267 / Rfactor Rwork: 0.165 / Total num. of bins used: 20
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 19 Å / Rfactor Rfree: 0.218 / Rfactor Rwork: 0.163
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.02
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.251
X-RAY DIFFRACTIONr_dihedral_angle_d
X-RAY DIFFRACTIONr_dihedral_angle_deg16.076

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