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- PDB-1or0: Crystal Structures of Glutaryl 7-Aminocephalosporanic Acid Acylas... -

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Basic information

Entry
Database: PDB / ID: 1or0
TitleCrystal Structures of Glutaryl 7-Aminocephalosporanic Acid Acylase: Insight into Autoproteolytic Activation
Components
  • Glutaryl 7-Aminocephalosporanic Acid Acylase
  • glutaryl acylase
KeywordsHYDROLASE / Glutaryl 7-aminocephalosporanic acid / N-terminal nucleophile (Ntn) hydrolases / Glutaryl 7-aminocephalosporanic acid 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 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 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 / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Glutaryl-7-aminocephalosporanic-acid acylase / Glutaryl-7-aminocephalosporanic-acid acylase
Similarity search - Component
Biological speciesPseudomonas sp. SY-77-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsKim, J.K. / Yang, I.S. / Rhee, S. / Dauter, Z. / Lee, Y.S. / Park, S.S. / Kim, K.H.
CitationJournal: Biochemistry / Year: 2003
Title: Crystal Structures of Glutaryl 7-Aminocephalosporanic Acid Acylase: Insight into Autoproteolytic Activation
Authors: Kim, J.K. / Yang, I.S. / Rhee, S. / Dauter, Z. / Lee, Y.S. / Park, S.S. / Kim, K.H.
History
DepositionMar 11, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Glutaryl 7-Aminocephalosporanic Acid Acylase
B: glutaryl acylase
C: Glutaryl 7-Aminocephalosporanic Acid Acylase
D: glutaryl acylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,6626
Polymers154,5384
Non-polymers1242
Water25,7431429
1
A: Glutaryl 7-Aminocephalosporanic Acid Acylase
B: glutaryl acylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3313
Polymers77,2692
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8120 Å2
ΔGint-49 kcal/mol
Surface area24670 Å2
MethodPISA
2
C: Glutaryl 7-Aminocephalosporanic Acid Acylase
D: glutaryl acylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3313
Polymers77,2692
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8090 Å2
ΔGint-50 kcal/mol
Surface area24660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)229.667, 69.907, 113.726
Angle α, β, γ (deg.)90.00, 97.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glutaryl 7-Aminocephalosporanic Acid Acylase


Mass: 17644.172 Da / Num. of mol.: 2 / Fragment: alpha subunit, RESIDUES 1-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. SY-77-1 (bacteria) / Strain: GK16 / Plasmid: pET23a / Production host: Escherichia coli (E. coli)
References: UniProt: Q84I62, UniProt: P07662*PLUS, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein glutaryl acylase / Glutaryl 7-Aminocephalosporanic Acid Acylase


Mass: 59624.598 Da / Num. of mol.: 2 / Fragment: beta subunit, RESIDUES 1-522
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. SY-77-1 (bacteria) / Strain: GK16 / Plasmid: pET23a / Production host: Escherichia coli (E. coli)
References: UniProt: Q84I62, UniProt: P07662*PLUS, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1429 / 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: 2.93 Å3/Da / Density % sol: 57.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.6M ammonium sulfate, 0.1M HEPES, and 0.1M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.6 Mammonium sulfate1reservoir
20.1 MHEPES1reservoirpH7.5
30.1 M1reservoirNaCl

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9810, 0.9800, 0.9680
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9811
20.981
30.9681
ReflectionResolution: 2→19.95 Å / Num. obs: 217224 / % possible obs: 91.8 %
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. obs: 110770

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2→19.95 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.184 8392 0.2113 %RANDOM
Rwork0.171 ---
obs0.189 217224 91.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.824 Å2 / ksol: 0.389707 e/Å3
Displacement parametersBiso mean: 14.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.65 Å20 Å2-1.9 Å2
2--3.38 Å20 Å2
3----0.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10609 0 8 1429 12046
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.921.5
X-RAY DIFFRACTIONc_mcangle_it1.312
X-RAY DIFFRACTIONc_scbond_it1.822
X-RAY DIFFRACTIONc_scangle_it2.532.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.21 1291 3.9 %
Rwork0.212 32046 -
obs--84.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3EG.PARAMEG.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. reflection obs: 110770 / Num. reflection Rfree: 4488 / % reflection Rfree: 4 % / Rfactor Rfree: 0.206 / Rfactor Rwork: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9

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