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- PDB-1k7d: Penicillin Acylase with Phenyl Proprionic Acid -

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Basic information

Entry
Database: PDB / ID: 1k7d
TitlePenicillin Acylase with Phenyl Proprionic Acid
Components
  • Penicillin Acylase alpha subunit
  • penicillin Acylase beta subunit
KeywordsHYDROLASE / NTN-HYDROLASE FOLD / HELICES / BETA-STRANDS / Phenyl Proprionic acid
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
R-2-PHENYL-PROPRIONIC ACID / Penicillin G acylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 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 19, 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 / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 16, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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
Revision 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_distant_solvent_atoms / pdbx_entry_details ...pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Penicillin Acylase alpha subunit
B: penicillin Acylase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4594
Polymers86,2682
Non-polymers1902
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14540 Å2
ΔGint-96 kcal/mol
Surface area28240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.331, 64.551, 64.347
Angle α, β, γ (deg.)72.54, 73.29, 73.58
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Penicillin 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 Acylase beta subunit / PENICILLIN G AMIDASE / PENICILLIN G AMIDOHYDROLASE


Mass: 62429.496 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
#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


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.12 Å3/Da / Density % sol: 41.6 %
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: MACSCIENCE / Detector: IMAGE PLATE / Date: Jan 1, 2000 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. all: 40070 / Num. obs: 38187 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Redundancy: 1.74 % / Biso Wilson estimate: 34.5 Å2 / Rsym value: 0.068 / Net I/σ(I): 10.1
Reflection shellResolution: 2.15→2.19 Å / Mean I/σ(I) obs: 2.7 / Rsym value: 0.229 / % possible all: 87.5
Reflection
*PLUS
Num. obs: 36555 / % possible obs: 96.7 % / Num. measured all: 64473 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
Highest resolution: 2.14 Å / % possible obs: 87.5 % / Rmerge(I) obs: 0.229 / Mean I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
REFMAC5refinement
SCALEPACKdata scaling
TRUNCATEdata reduction
CNSrefinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PNK

1pnk


Resolution: 2.15→30.15 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.917 / SU B: 8.026 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.307 / ESU R Free: 0.2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.21646 1632 4.3 %RANDOM
Rwork0.18215 ---
obs0.18376 36555 91.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 22.081 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å2-0.3 Å20.05 Å2
2---0.04 Å2-0.04 Å2
3---0.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.15→30.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6072 0 12 319 6403
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0216251
X-RAY DIFFRACTIONr_bond_other_d0.0010.025406
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.9228513
X-RAY DIFFRACTIONr_angle_other_deg0.88312604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.073761
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.201151068
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0970.2898
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027050
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021294
X-RAY DIFFRACTIONr_nbd_refined0.2380.31365
X-RAY DIFFRACTIONr_nbd_other0.2140.35423
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1240.51
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.5422
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.020.52
X-RAY DIFFRACTIONr_metal_ion_refined0.0980.54
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4540.314
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2140.344
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3710.516
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.751.53798
X-RAY DIFFRACTIONr_mcangle_it1.34726116
X-RAY DIFFRACTIONr_scbond_it2.1532453
X-RAY DIFFRACTIONr_scangle_it3.4294.52397
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellHighest resolution: 2.15 Å / Rfactor Rfree: 0.286 / Rfactor Rwork: 0.222 / Total num. of bins used: 20
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.216 / Rfactor Rwork: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.589
X-RAY DIFFRACTIONr_dihedral_angle_d
X-RAY DIFFRACTIONr_dihedral_angle_deg18.9

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