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- PDB-3ml0: Thermostable Penicillin G acylase from Alcaligenes faecalis in te... -

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Basic information

Entry
Database: PDB / ID: 3ml0
TitleThermostable Penicillin G acylase from Alcaligenes faecalis in tetragonal form
Components
  • Penicillin G acylase, alpha subunit
  • Penicillin G acylase, beta subunit
KeywordsHYDROLASE / penicillin G acylase
Function / homology
Function and homology information


penicillin amidase / penicillin amidase activity / antibiotic biosynthetic process / 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
Penicillin G acylase
Similarity search - Component
Biological speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.5 Å
AuthorsVarshney, N.K. / Kumar, R.S. / Ignatova, Z. / Dodson, E. / Suresh, C.G.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Crystallization and X-ray structure analysis of a thermostable penicillin G acylase from Alcaligenes faecalis.
Authors: Varshney, N.K. / Kumar, R.S. / Ignatova, Z. / Prabhune, A. / Pundle, A. / Dodson, E. / Suresh, C.G.
History
DepositionApr 16, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 14, 2012Group: Database references / Structure summary
Revision 1.3Dec 18, 2019Group: Advisory / Database references
Category: citation / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Nov 1, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)85,0913
Polymers85,0512
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13010 Å2
ΔGint-76 kcal/mol
Surface area29890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.558, 85.558, 298.804
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Penicillin G acylase, alpha subunit / Penicillin G amidase


Mass: 22258.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Gene: pac / Plasmid: pPAAF / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 alpha / References: UniProt: O34142, penicillin amidase
#2: Protein Penicillin G acylase, beta subunit / Penicillin G amidase


Mass: 62791.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Gene: pac / Plasmid: pPAAF / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 alpha / References: UniProt: O34142, penicillin amidase
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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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: 3.22 Å3/Da / Density % sol: 61.74 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG 8000, 0.1M Tris-Hcl pH7.5, 100uL b-octyl-glucopyranoside (0.50% w/v), vapor diffusion, hanging drop, temperature 303K

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.514 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 7, 2006 / Details: Mirrors
RadiationMonochromator: Osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 3.5→82.2 Å / Num. obs: 14860 / % possible obs: 90.8 % / Observed criterion σ(F): 1 / Redundancy: 2.25 % / Biso Wilson estimate: 29.99 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 7.42
Reflection shellResolution: 3.499→3.59 Å / Redundancy: 2.01 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 3.08 / Num. unique all: 13376 / % possible all: 89.67

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0072refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GK9

1gk9


Resolution: 3.5→20 Å / Cor.coef. Fo:Fc: 0.849 / Cor.coef. Fo:Fc free: 0.823 / Occupancy max: 1 / Occupancy min: 0 / SU B: 35.918 / SU ML: 0.547 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.716 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.283 680 5.1 %RANDOM
Rwork0.269 ---
all0.313 14860 --
obs0.269 13376 90.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 65.2 Å2 / Biso mean: 47.781 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-3.93 Å20 Å20 Å2
2--3.93 Å20 Å2
3----7.86 Å2
Refinement stepCycle: LAST / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5995 0 1 0 5996
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0226138
X-RAY DIFFRACTIONr_angle_refined_deg0.7241.938346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0865741
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80424.062325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26715964
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.41545
X-RAY DIFFRACTIONr_chiral_restr0.0470.2854
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214882
X-RAY DIFFRACTIONr_mcbond_it0.0751.53710
X-RAY DIFFRACTIONr_mcangle_it0.13425971
X-RAY DIFFRACTIONr_scbond_it0.04732428
X-RAY DIFFRACTIONr_scangle_it0.0844.52375
LS refinement shellResolution: 3.499→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 50 -
Rwork0.343 914 -
all-964 -
obs-964 89.67 %

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