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- PDB-1keh: Precursor structure of cephalosporin acylase -

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Basic information

Entry
Database: PDB / ID: 1keh
TitlePrecursor structure of cephalosporin acylase
Componentsprecursor of cephalosporin acylase
KeywordsHYDROLASE / cephalosporin acylase / precursor / glutaryl-7-ACA
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 speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsKim, Y. / Kim, S.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Precursor structure of cephalosporin acylase. Insights into autoproteolytic activation in a new N-terminal hydrolase family
Authors: Kim, Y. / Kim, S. / Earnest, T.N. / Hol, W.G.
History
DepositionNov 16, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: precursor of cephalosporin acylase


Theoretical massNumber of molelcules
Total (without water)76,6101
Polymers76,6101
Non-polymers00
Water7,188399
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.700, 73.700, 381.000
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 precursor of cephalosporin acylase / Glutaryl 7-aminocephalosporanic acid acylase Precursor


Mass: 76609.883 Da / Num. of mol.: 1 / Fragment: residues 1-689 / Mutation: S170A,R428A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevundimonas diminuta (bacteria) / Plasmid: pET24d(+) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9L5D6, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 3.37 Å3/Da / Density % sol: 63.55 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG8000, MgAcetate, Sodium Cacodylate, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
250 mMsodium phosphate1droppH7.0
3150 mM1dropNaCl
420 %(w/v)PEG80001reservoir
510 mMdithiothreitol1reservoir
6200 mMmagnesium acetate1reservoir
7100 mMsodium cacodylate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 125 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.91 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jan 7, 2001
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 39792 / Num. obs: 38001 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3.2
Reflection shellResolution: 2.5→2.59 Å / % possible all: 70.4
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 838095 / Rmerge(I) obs: 0.108
Reflection shell
*PLUS
Highest resolution: 2.5 Å / % possible obs: 70.4 % / Rmerge(I) obs: 0.548 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.5→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1024 3.08 %random
Rwork0.203 ---
all0.205 37695 --
obs0.205 33229 --
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5374 0 0 399 5773
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 3.5 % / Rfactor obs: 0.203
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.0067
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.32

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