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- PDB-3k3w: Thermostable Penicillin G acylase from Alcaligenes faecalis in or... -

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Basic information

Entry
Database: PDB / ID: 3k3w
TitleThermostable Penicillin G acylase from Alcaligenes faecalis in orthorhombic form
Components(Penicillin G acylase) x 2
KeywordsHYDROLASE / penicillin G acylase
Function / homology
Function and homology information


penicillin amidase activity / penicillin amidase / antibiotic biosynthetic process / 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
Penicillin G acylase
Similarity search - Component
Biological speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.31 Å
AuthorsVarshney, N.K. / Kumar, R.S. / Ignatova, Z. / Dodson, E. / Suresh, C.G.
Citation
Journal: 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.
#1: Journal: Eur.J.Biochem. / Year: 2003
Title: Fragments of pro-peptide activate mature penicillin amidase of Alcaligenes faecalis
Authors: Kasche, V. / Galunsky, B. / Ignatova, Z.
History
DepositionOct 5, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 14, 2012Group: Database references / Structure summary
Revision 1.3Jan 1, 2020Group: 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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Penicillin G acylase
B: Penicillin G acylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1623
Polymers85,1222
Non-polymers401
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12930 Å2
ΔGint-90 kcal/mol
Surface area29720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.929, 86.016, 260.181
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Penicillin G acylase / Penicillin G amidase precursor


Mass: 22329.963 Da / Num. of mol.: 1 / Fragment: UNP residues 27-222
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Gene: pac / Plasmid: pPAAF / Production host: Escherichia coli (E. coli) / References: UniProt: O34142, penicillin amidase
#2: Protein Penicillin G acylase / Penicillin G amidase precursor


Mass: 62791.953 Da / Num. of mol.: 1 / Fragment: UNP residues 266-816
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Gene: pac / Plasmid: pPAAF / Production host: Escherichia coli (E. coli) / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.68 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG8000, 0.1M Tris-Hcl, pH7.5, 60uL of b-octyl- glucopyranoside (0.50% w/v), VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.514 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 1, 2007 / 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: 3.306→46.823 Å / Num. all: 12626 / Num. obs: 12602 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Redundancy: 5.73 % / Biso Wilson estimate: 33.34 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 9.23
Reflection shellResolution: 3.31→3.39 Å / Redundancy: 5.07 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 4.81 / Num. unique all: 806 / % possible all: 96.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0072refinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GK9

1gk9


Resolution: 3.31→46.82 Å / Cor.coef. Fo:Fc: 0.822 / Cor.coef. Fo:Fc free: 0.779 / Occupancy max: 1 / Occupancy min: 0 / SU B: 41.193 / SU ML: 0.69 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.747 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.315 613 4.9 %RANDOM
Rwork0.281 ---
obs0.283 11989 99.7 %-
all-12647 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 99.99 Å2 / Biso mean: 40.97 Å2 / Biso min: 15.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 3.31→46.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6000 0 1 10 6011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226122
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8751.9298321
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2625741
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.74424.087323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.85315961
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6821544
X-RAY DIFFRACTIONr_chiral_restr0.0630.2850
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214869
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
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_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2671.53706
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.47125957
X-RAY DIFFRACTIONr_scbond_it0.07232416
X-RAY DIFFRACTIONr_scangle_it0.1284.52364
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.31→3.39 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 45 -
Rwork0.312 804 -
all-851 -
obs-806 96.81 %

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