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- PDB-1c3b: AMPC BETA-LACTAMASE FROM E. COLI COMPLEXED WITH INHIBITOR, BENZO(... -

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Basic information

Entry
Database: PDB / ID: 1c3b
TitleAMPC BETA-LACTAMASE FROM E. COLI COMPLEXED WITH INHIBITOR, BENZO(B)THIOPHENE-2-BORONIC ACID (BZB)
ComponentsCEPHALOSPORINASE
KeywordsHYDROLASE / CEPHALOSPORINASE / BETA-LACTAMASE / SERINE HYDROLASE
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase activity / beta-lactamase / outer membrane-bounded periplasmic space / response to antibiotic
Similarity search - Function
Beta-lactamase, class-C active site / Beta-lactamase class-C active site. / : / Beta-lactamase-related / Beta-lactamase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BENZO[B]THIOPHENE-2-BORONIC ACID / Beta-lactamase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsPowers, R.A. / Blazquez, J. / Weston, G.S. / Morosini, M.I. / Baquero, F. / Shoichet, B.K.
CitationJournal: Protein Sci. / Year: 1999
Title: The complexed structure and antimicrobial activity of a non-beta-lactam inhibitor of AmpC beta-lactamase.
Authors: Powers, R.A. / Blazquez, J. / Weston, G.S. / Morosini, M.I. / Baquero, F. / Shoichet, B.K.
History
DepositionJul 27, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CEPHALOSPORINASE
B: CEPHALOSPORINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5324
Polymers79,1762
Non-polymers3562
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.859, 78.012, 98.962
Angle α, β, γ (deg.)90.00, 116.066, 90.00
Int Tables number5
Space group name H-MC121
DetailsChain A and B each represent monomers that assemble into a homodimer in the asymmetric unit. The biological unit is the monomer.

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Components

#1: Protein CEPHALOSPORINASE


Mass: 39587.922 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: POGO295 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00811, beta-lactamase
#2: Chemical ChemComp-BZB / BENZO[B]THIOPHENE-2-BORONIC ACID


Mass: 178.016 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H7BO2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.6 Å3/Da / Density % sol: 52.71 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 1.7M potassium phosphate, 360uM benzo(b)thiophene-2-boronic acid, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Temperature: 23 ℃ / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.7 Mpotassium phosphate1reservoir
20.100 mMprotein1drop
30.360 mMinhibitor1drop
42 %DMSO1drop
51.7 Mpotassium phosphate1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 6, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. all: 33738 / Num. obs: 33738 / % possible obs: 86.6 % / Observed criterion σ(I): -3 / Redundancy: 1.8 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 11.4
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.137 / Num. unique all: 4237 / % possible all: 76.3
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 76.4 %

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.25→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 3287 9.9 %RANDOM
Rwork0.167 ---
obs0.167 33287 86.1 %-
all-33737 --
Displacement parametersBiso mean: 26.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5590 0 24 94 5708
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.78
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.171.5
X-RAY DIFFRACTIONx_mcangle_it3.232
X-RAY DIFFRACTIONx_scbond_it4.262
X-RAY DIFFRACTIONx_scangle_it6.462.5
LS refinement shellResolution: 2.25→2.35 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.277 340 9.4 %
Rwork0.227 3289 -
obs--76 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2BZB.PARAMBZB.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 9.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.78
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.277 / % reflection Rfree: 9.4 % / Rfactor Rwork: 0.227

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