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- PDB-2ae5: Glutaryl 7-Aminocephalosporanic Acid Acylase: mutational study of... -

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Basic information

Entry
Database: PDB / ID: 2ae5
TitleGlutaryl 7-Aminocephalosporanic Acid Acylase: mutational study of activation mechanism
Components(Glutaryl 7-Aminocephalosporanic Acid Acylase) x 2
KeywordsHYDROLASE / autoproteolysis / precursor activation / intermediate structure / cephalosporin acylase
Function / homology
Function and homology information


glutaryl-7-aminocephalosporanic-acid acylase / glutaryl-7-aminocephalosporanic-acid acylase activity / antibiotic biosynthetic process / periplasmic space / response to antibiotic
Similarity search - Function
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 (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 / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glutaryl-7-aminocephalosporanic-acid acylase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsKim, J.K. / Yang, I.S. / Shin, H.J. / Cho, K.J. / Ryu, E.K. / Kim, S.H. / Park, S.S. / Kim, K.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2006
Title: Insight into autoproteolytic activation from the structure of cephalosporin acylase: a protein with two proteolytic chemistries.
Authors: Kim, J.K. / Yang, I.S. / Shin, H.J. / Cho, K.J. / Ryu, E.K. / Kim, S.H. / Park, S.S. / Kim, K.H.
History
DepositionJul 21, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Glutaryl 7-Aminocephalosporanic Acid Acylase
B: Glutaryl 7-Aminocephalosporanic Acid Acylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5794
Polymers77,3912
Non-polymers1882
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint-76 kcal/mol
Surface area25560 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)73.736, 73.736, 383.349
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 Glutaryl 7-Aminocephalosporanic Acid Acylase


Mass: 18205.922 Da / Num. of mol.: 1 / Fragment: alpha domain(residues 1-166)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Species: Pseudomonas sp. SY-77-1 / Strain: GK16 / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / References: UniProt: P07662*PLUS, penicillin amidase
#2: Protein Glutaryl 7-Aminocephalosporanic Acid Acylase


Mass: 59184.895 Da / Num. of mol.: 1 / Fragment: beta domain(residues 1-522) / Mutation: S1C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Species: Pseudomonas sp. SY-77-1 / Strain: GK16 / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / References: UniProt: P07662*PLUS, penicillin amidase
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / 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: 3.4 Å3/Da / Density % sol: 63.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 8000, Tris, magnesium chloride, cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 23, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.1→95.35 Å / Num. obs: 57515 / % possible obs: 90.5 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.095 / Χ2: 1.081
Reflection shellResolution: 2.1→2.18 Å / % possible obs: 81 % / Redundancy: 5 % / Rmerge(I) obs: 0.453 / Num. measured obs: 5028 / Χ2: 0.902

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Phasing

Phasing MRMethod rotation: fast direct
Phasing dm shellResolution: 1.97→50 Å / Delta phi final: 0.162 / FOM : 0.172 / Reflection: 63977

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
REFMAC5.1.24refinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.365 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.209 2472 5.1 %RANDOM
Rwork0.173 ---
all0.175 ---
obs-48502 92.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.787 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20 Å2
2--0.78 Å20 Å2
3----1.55 Å2
Refinement stepCycle: LAST / Resolution: 2.24→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5363 0 11 382 5756
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0215527
X-RAY DIFFRACTIONr_bond_other_d0.0020.024828
X-RAY DIFFRACTIONr_angle_refined_deg1.2311.9337548
X-RAY DIFFRACTIONr_angle_other_deg0.827311179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0185678
X-RAY DIFFRACTIONr_chiral_restr0.0760.2787
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026314
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021208
X-RAY DIFFRACTIONr_nbd_refined0.2010.21034
X-RAY DIFFRACTIONr_nbd_other0.2380.25579
X-RAY DIFFRACTIONr_nbtor_other0.0810.22998
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2291
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0960.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2610.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0580.23
X-RAY DIFFRACTIONr_mcbond_it0.6161.53401
X-RAY DIFFRACTIONr_mcangle_it1.10325470
X-RAY DIFFRACTIONr_scbond_it1.47232126
X-RAY DIFFRACTIONr_scangle_it2.4124.52078
X-RAY DIFFRACTIONr_rigid_bond_restr0.83325527
X-RAY DIFFRACTIONr_sphericity_free2.3962382
X-RAY DIFFRACTIONr_sphericity_bonded0.9525373
LS refinement shellResolution: 2.24→2.298 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.256 161
Rwork0.207 2983
all-3144

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