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- PDB-3jtr: Mutations in Cephalosporin Acylase Affecting Stability and Autopr... -

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Basic information

Entry
Database: PDB / ID: 3jtr
TitleMutations in Cephalosporin Acylase Affecting Stability and Autoproteolysis
Components(Glutaryl 7-aminocephalosporanic acid acylase) x 2
KeywordsHYDROLASE / Cephalosporin Acylase / Autoproteolysis
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / antibiotic biosynthetic process / periplasmic space
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: 2.5 Å
AuthorsCho, K.J. / Kim, J.K. / Lee, J.H. / Shin, H.J. / Park, S.S. / Kim, K.H.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Structural features of cephalosporin acylase reveal the basis of autocatalytic activation.
Authors: Cho, K.J. / Kim, J.K. / Lee, J.H. / Shin, H.J. / Park, S.S. / Kim, K.H.
History
DepositionSep 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)77,7363
Polymers77,6442
Non-polymers921
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8350 Å2
ΔGint-53 kcal/mol
Surface area25530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.816, 73.816, 381.324
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Glutaryl 7-aminocephalosporanic acid acylase


Mass: 18475.178 Da / Num. of mol.: 1 / Fragment: UNP residues 30-198 / Mutation: Q168P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: GK16 / Plasmid: pET23d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A4ZVL3, glutaryl-7-aminocephalosporanic-acid acylase
#2: Protein Glutaryl 7-aminocephalosporanic acid acylase


Mass: 59168.832 Da / Num. of mol.: 1 / Fragment: UNP residues 199-720
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: GK16 / Plasmid: pET23d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A4ZVL3, glutaryl-7-aminocephalosporanic-acid acylase
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE DEPOSITORS STATE THAT UNIPROT IS INCORRECT AT THESE POSITIONS

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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: 3.34 Å3/Da / Density % sol: 63.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Na-cacodylate (pH 6.5), 0.2M magnesium chloride, PEG 3000, 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: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 29, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 37974 / Num. obs: 34291 / % possible obs: 90.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 24.3
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 12.7 / % possible all: 79.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ADV

2adv


Resolution: 2.5→19.5 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.911 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 16.245 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1711 5 %RANDOM
Rwork0.182 ---
obs0.184 34221 90.42 %-
all-37847 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.97 Å2 / Biso mean: 27.609 Å2 / Biso min: 4.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5355 0 6 255 5616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225519
X-RAY DIFFRACTIONr_angle_refined_deg1.3121.9427540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2755678
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4823.238281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10915792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6111550
X-RAY DIFFRACTIONr_chiral_restr0.0910.2787
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024440
X-RAY DIFFRACTIONr_nbd_refined0.2060.22666
X-RAY DIFFRACTIONr_nbtor_refined0.310.23758
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2322
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.26
X-RAY DIFFRACTIONr_mcbond_it0.6141.53474
X-RAY DIFFRACTIONr_mcangle_it1.04725471
X-RAY DIFFRACTIONr_scbond_it1.43832362
X-RAY DIFFRACTIONr_scangle_it2.2614.52069
X-RAY DIFFRACTIONr_rigid_bond_restr0.97735836
X-RAY DIFFRACTIONr_sphericity_free4.7293255
X-RAY DIFFRACTIONr_sphericity_bonded1.65435363
LS refinement shellResolution: 2.5→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 105 -
Rwork0.273 2028 -
all-2133 -
obs--79.23 %

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