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- PDB-1fxh: MUTANT OF PENICILLIN ACYLASE IMPAIRED IN CATALYSIS WITH PHENYLACE... -

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Basic information

Entry
Database: PDB / ID: 1fxh
TitleMUTANT OF PENICILLIN ACYLASE IMPAIRED IN CATALYSIS WITH PHENYLACETIC ACID IN THE ACTIVE SITE
Components(PENICILLIN ACYLASE) x 2
KeywordsHYDROLASE / Ntn-hydrolase fold
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 / SYNCHROTRON / Resolution: 1.97 Å
AuthorsAlkema, W.B. / Hensgens, C.M. / Kroezinga, E.H. / de Vries, E. / Floris, R. / van der Laan, J.M. / Dijkstra, B.W. / Janssen, D.B.
CitationJournal: Protein Eng. / Year: 2000
Title: Characterization of the beta-lactam binding site of penicillin acylase of Escherichia coli by structural and site-directed mutagenesis studies.
Authors: Alkema, W.B. / Hensgens, C.M. / Kroezinga, E.H. / de Vries, E. / Floris, R. / van der Laan, J.M. / Dijkstra, B.W. / Janssen, D.B.
History
DepositionSep 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PENICILLIN ACYLASE
B: PENICILLIN ACYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4164
Polymers86,2392
Non-polymers1762
Water11,764653
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14390 Å2
ΔGint-98 kcal/mol
Surface area27860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.014, 64.084, 64.225
Angle α, β, γ (deg.)72.92, 73.91, 73.54
Int Tables number1
Space group name H-MP1
DetailsThe biological assembly is a hetero dimer.

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Components

#1: Protein PENICILLIN ACYLASE


Mass: 23838.824 Da / Num. of mol.: 1 / Fragment: ALPHA SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PEC / Production host: Escherichia coli (E. coli) / References: UniProt: P06875, penicillin amidase
#2: Protein PENICILLIN ACYLASE


Mass: 62400.496 Da / Num. of mol.: 1 / Fragment: BETA SUBUNIT / Mutation: N241A, V148L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PEC / Production host: Escherichia coli (E. coli) / 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-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.: 653 / 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: 2.18 Å3/Da / Density % sol: 43.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PEG MME 2000, MOPS, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Details: drop consists of equal amounts of protein and precipitant solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
18 mg/mlenzyme1drop
212-15 %mPEG20001reservoirprecipitant
350 mMMOPS1reservoirprecipitant

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.04
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 25, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.97→20 Å / Num. all: 51862 / Num. obs: 50404 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 5.7 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 15.7
Reflection shellResolution: 1.97→2 Å / Rmerge(I) obs: 0.124 / Num. unique all: 0 / % possible all: 95
Reflection shell
*PLUS
% possible obs: 95 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
RefinementResolution: 1.97→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER / Details: USED MAXIMUM LIKELYHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2567 -RANDOM
Rwork0.181 ---
obs0.181 50128 5.1 %-
all-51862 --
Refinement stepCycle: LAST / Resolution: 1.97→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6069 0 11 653 6733
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_torsion_deg22.9
X-RAY DIFFRACTIONc_torsion_impr_deg0.72
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.72

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