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- PDB-1fm2: THE 2 ANGSTROM CRYSTAL STRUCTURE OF CEPHALOSPORIN ACYLASE -

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Basic information

Entry
Database: PDB / ID: 1fm2
TitleTHE 2 ANGSTROM CRYSTAL STRUCTURE OF CEPHALOSPORIN ACYLASE
Components(GLUTARYL 7-AMINOCEPHALOSPORANIC ACID ACYLASE) x 2
KeywordsHYDROLASE / cephalosporin acylase / antibiotics / penicillin acylase / N-terminal hydrolase
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 / Resolution: 2 Å
AuthorsKim, Y. / Yoon, K.H. / Khang, Y. / Turley, S. / Hol, W.G.J.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: The 2.0 A crystal structure of cephalosporin acylase.
Authors: Kim, Y. / Yoon, K. / Khang, Y. / Turley, S. / Hol, W.G.
History
DepositionAug 15, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

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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


Theoretical massNumber of molelcules
Total (without water)77,2532
Polymers77,2532
Non-polymers00
Water7,602422
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-55 kcal/mol
Surface area24830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.6, 73.6, 380.9
Angle α, β, γ (deg.)90, 90, 90
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein GLUTARYL 7-AMINOCEPHALOSPORANIC ACID ACYLASE / CEPHALOSPORIN ACYLASE


Mass: 18567.113 Da / Num. of mol.: 1 / Fragment: ALPHA SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevundimonas diminuta (bacteria) / Plasmid: PET SYSTEM / Production host: Escherichia coli (E. coli) / References: UniProt: Q9L5D6
#2: Protein GLUTARYL 7-AMINOCEPHALOSPORANIC ACID ACYLASE / CEPHALOSPORIN ACYLASE


Mass: 58686.363 Da / Num. of mol.: 1 / Fragment: BETA SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brevundimonas diminuta (bacteria) / Plasmid: PET SYSTEM / Production host: Escherichia coli (E. coli) / References: UniProt: Q9L5D6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 422 / 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: 3.34 Å3/Da / Density % sol: 63.13 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6.5
Details: 20% PEG8000, 200 mM MgAcetate, 100 mM NaCacodylate, 10 mM DTT, pH 6.5, VAPOR DIFFUSION, temperature 21K
Crystal
*PLUS
Density % sol: 57 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
250 mMsodium phosphate1drop
3150 mM1dropNaCl
420 %(w/v)PEG80001reservoir
510 mMdithiothreitol1reservoir
6200 mMmagnesium acetate1reservoir
7100 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.0000, 0.96410, 0.97820, 0.97946
DetectorType: OTHER / Detector: CCD / Date: Sep 8, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.96411
30.97821
40.979461
ReflectionResolution: 2→40 Å / Num. all: 134878 / Num. obs: 124497 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 4.2 / Redundancy: 1.5 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 12.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.216 / Num. unique all: 13438 / % possible all: 88.9
Reflection
*PLUS
Num. measured all: 190883
Reflection shell
*PLUS
% possible obs: 88.9 % / Mean I/σ(I) obs: 4.2

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2→40 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.23 3316 random
Rwork0.208 --
all0.213 72386 -
obs0.21 65919 -
Refinement stepCycle: LAST / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5298 0 0 422 5720
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 40 Å / σ(F): 0 / Rfactor obs: 0.208 / Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS

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