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- PDB-1jvz: Structure of cephalosporin acylase in complex with glutaryl-7-ami... -

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Basic information

Entry
Database: PDB / ID: 1jvz
TitleStructure of cephalosporin acylase in complex with glutaryl-7-aminocephalosporanic acid
Components
  • cephalosporin acylase alpha chain
  • cephalosporin acylase beta chain
KeywordsHYDROLASE / cephalosporin acylase / glutaryl-7-aminocephalosporanic acid
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
7BETA-(4CARBOXYBUTANAMIDO) CEPHALOSPORANIC ACID / Glutaryl-7-aminocephalosporanic-acid acylase
Similarity search - Component
Biological speciesBrevundimonas diminuta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsKim, Y. / Hol, W.G.J.
CitationJournal: CHEM.BIOL. / Year: 2001
Title: Structure of cephalosporin acylase in complex with glutaryl-7-aminocephalosporanic acid and glutarate: insight into the basis of its substrate specificity
Authors: Kim, Y. / Hol, W.G.
History
DepositionSep 1, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 1, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 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 / 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.pdbx_seq_one_letter_code / _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: cephalosporin acylase alpha chain
B: cephalosporin acylase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5453
Polymers76,1582
Non-polymers3861
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint-56 kcal/mol
Surface area24920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.140, 74.140, 379.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Detailsheterodimer of one alpha and one beta chains

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Components

#1: Protein cephalosporin acylase alpha chain / glutaryl 7-aminocephalosporanic acid acylase


Mass: 17472.033 Da / Num. of mol.: 1 / Fragment: RESIDUES 30-187
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
#2: Protein cephalosporin acylase beta chain / glutaryl 7-aminocephalosporanic acid acylase


Mass: 58686.363 Da / Num. of mol.: 1 / Fragment: RESIDUES 199-718
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
#3: Chemical ChemComp-CEN / 7BETA-(4CARBOXYBUTANAMIDO) CEPHALOSPORANIC ACID / GLUTARYL 7-AMINO CEPHALOSPORANIC ACID


Mass: 386.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H18N2O8S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 3.42 Å3/Da / Density % sol: 64.08 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG8000, MgAcetate, NaCacodylate, DTT, pH 5.5, 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 mMGL-7-ACA1drop
520 %(w/v)PEG80001reservoir
610 mMdithiothreitol1reservoir
7200 mMmagnesium acetate1reservoir
8100 mMsodium cacodylate1reservoirpH5.5

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Data collection

DiffractionMean temperature: 125 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.0332 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 24, 2000
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 33008 / Num. obs: 32457 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.98 / Redundancy: 6 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.9
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.587 / % possible all: 92.1
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 98.3 % / Num. measured all: 196351 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Highest resolution: 2.6 Å / % possible obs: 92.1 % / Mean I/σ(I) obs: 1.98

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.6→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1064 3.5 %random
Rwork0.19 ---
all0.192 30704 --
obs0.192 30704 --
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5299 0 26 416 5741
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.27
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.213 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.006

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