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- PDB-1cef: CEFOTAXIME COMPLEXED WITH THE STREPTOMYCES R61 DD-PEPTIDASE -

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Basic information

Entry
Database: PDB / ID: 1cef
TitleCEFOTAXIME COMPLEXED WITH THE STREPTOMYCES R61 DD-PEPTIDASE
ComponentsD-ALANYL-D-ALANINE CARBOXYPEPTIDASE TRANSPEPTIDASE
KeywordsHYDROLASE-TRANSPEPTIDASE / D-AMINO ACID PEPTIDASE / PENICILLIN TARGET
Function / homology
Function and homology information


serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / proteolysis / extracellular region
Similarity search - Function
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
CEFOTAXIME, C3' cleaved, open, bound form / D-alanyl-D-alanine carboxypeptidase
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.04 Å
AuthorsKnox, J.R. / Kuzin, A.P.
Citation
Journal: Biochemistry / Year: 1995
Title: Binding of cephalothin and cefotaxime to D-ala-D-ala-peptidase reveals a functional basis of a natural mutation in a low-affinity penicillin-binding protein and in extended-spectrum beta-lactamases.
Authors: Kuzin, A.P. / Liu, H. / Kelly, J.A. / Knox, J.R.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: The Refined Crystallographic Structure of a Dd-Peptidase Penicillin-Target Enzyme at 1.6 A Resolution
Authors: Kelly, J.A. / Kuzin, A.P.
#2: Journal: J.Mol.Biol. / Year: 1989
Title: Crystallographic Mapping of Beta-Lactams Bound to a D-Alanyl-D-Alanine Peptidase Target Enzyme
Authors: Kelly, J.A. / Knox, J.R. / Zhao, H. / Frere, J.M. / Ghaysen, J.M.
#3: Journal: Science / Year: 1986
Title: On the Origin of Bacterial Resistance to Penicillin: Comparison of a Beta-Lactamase and a Penicillin Target
Authors: Kelly, J.A. / Dideberg, O. / Charlier, P. / Wery, J.P. / Libert, M. / Moews, P.C. / Knox, J.R. / Duez, C. / Fraipont, C. / Joris, B. / al., et
#4: Journal: J.Biol.Chem. / Year: 1985
Title: 2.8-A Structure of Penicillin-Sensitive D-Alanyl Carboxypeptidase-Transpeptidase from Streptomyces R61 and Complexes with Beta-Lactams
Authors: Kelly, J.A. / Knox, J.R. / Moews, P.C. / Hite, G.J. / Bartolone, J.B. / Zhao, H. / Joris, B. / Frere, J.M. / Ghuysen, J.M.
History
DepositionJan 12, 1995-
Revision 1.0Oct 14, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE TRANSPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8202
Polymers37,4231
Non-polymers3971
Water4,432246
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.300, 67.300, 102.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein D-ALANYL-D-ALANINE CARBOXYPEPTIDASE TRANSPEPTIDASE / PENICILLIN TARGET


Mass: 37422.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces sp. (bacteria) / Strain: R61
References: UniProt: P15555, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-CEF / CEFOTAXIME, C3' cleaved, open, bound form / Cefotaxime


Mass: 397.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15N5O5S2 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.11 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlenzyme1drop
215 %(w/v)PEG80001drop
350 mMphosphate1drop
420 %(w/v)PEG80001reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Nov 29, 1989
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 19106 / % possible obs: 67 % / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Rmerge(I) obs: 0.057
Reflection
*PLUS
Highest resolution: 2.04 Å / Num. measured all: 38280

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Processing

Software
NameVersionClassification
XENGENdata collection
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata reduction
X-PLOR3.1phasing
RefinementResolution: 2.04→20 Å / σ(F): 3
Details: SEE STRUCTURE OF NATIVE FOR MULTIPLE CONFORMATIONS (J.A.KELLY AND A.P.KUZIN JOURNAL OF MOLECULAR BIOLOGY, 1995, SUBMITTED).
RfactorNum. reflection% reflection
Rfree0.24 -10 %
Rwork0.172 --
obs0.172 16066 74.5 %
Displacement parametersBiso mean: 6.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2.04→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2615 0 26 246 2887
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.009
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.8

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