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- PDB-1j9m: K38H mutant of Streptomyces K15 DD-transpeptidase -

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Basic information

Entry
Database: PDB / ID: 1j9m
TitleK38H mutant of Streptomyces K15 DD-transpeptidase
ComponentsDD-transpeptidase
KeywordsHYDROLASE / penicillin-binding / DD-transpeptidase / serine peptidase / beta-lactamase / hydrolase carboxypeptidase
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
Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal / Peptidase S11, D-alanyl-D-alanine carboxypeptidase A / D-alanyl-D-alanine carboxypeptidase / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-alanyl-D-alanine carboxypeptidase
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsFonze, E. / Rhazi, N. / Nguyen-Disteche, M. / Charlier, P.
Citation
Journal: Biochemistry / Year: 2003
Title: Catalytic mechanism of the Streptomyces K15 DD-transpeptidase/penicillin-binding protein probed by site-directed mutagenesis and structural analysis.
Authors: Rhazi, N. / Charlier, P. / Dehareng, D. / Engher, D. / Vermeire, M. / Frere, J.M. / Nguyen-Disteche, M. / Fonze, E.
#1: Journal: J.Biol.Chem. / Year: 1999
Title: The Crystal Structure of a Penicilloyl-Serine Transferase of Intermediate Penicillin Sensitivity
Authors: Fonze, E. / Vermeire, M. / Nguyen-Disteche, M. / Brasseur, R. / Charlier, P.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and X-Ray Diffraction Study of the Streptomyces K15 Penicillin-Binding DD-Transpeptidase
Authors: Englebert, S. / Charlier, P. / Fonze, E. / To'th, Y. / Vermeire, M. / Van Beeumen, J. / Grandchamps, J. / Hoffmann, K. / Leyh-Bouille, M. / Nguyen-Disteche, M. / Ghuysen, J.-M.
History
DepositionMay 28, 2001Deposition site: RCSB / Processing site: RCSB
SupersessionJun 13, 2001ID: 1EQS
Revision 1.0Jun 13, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 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: DD-transpeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5763
Polymers27,5171
Non-polymers582
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.596, 53.638, 104.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer

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Components

#1: Protein DD-transpeptidase /


Mass: 27517.287 Da / Num. of mol.: 1 / Mutation: K38H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Strain: K15 / Species (production host): Streptomyces lividans / Production host: Streptomyces lividans TK24 (bacteria) / Strain (production host): TK24
References: UniProt: P39042, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.33 Å3/Da / Density % sol: 47.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: Tris 0.1 M, PEG 6K 30%, NaCl 0.4 M, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.3-20 mg/mlprotein1drop
20.1 MTris-HCl1reservoir
30.5 M1reservoirNaCl
4PEG60001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.56→34.71 Å / Num. all: 37427 / Num. obs: 34332 / % possible obs: 85.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 19.13
Reflection shellResolution: 1.56→1.6 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.139 / % possible all: 39.7
Reflection
*PLUS
% possible obs: 91.7 %
Reflection shell
*PLUS
% possible obs: 39.7 % / Num. unique obs: 1069 / Mean I/σ(I) obs: 4.1

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Processing

Software
NameVersionClassification
XDSdata reduction
AMoREphasing
X-PLOR3.851refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→8 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / σ(F): 2
Details: THE ELECTRON DENSITY FOR RESIDUES ILE 145, GLY 146 and ASN 147 IS NOT WELL-DEFINED. THOSE RESIDUES WERE EXCLUDED FROM THE REFINEMENT PROCESS.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1529 5 %RANDOM
Rwork0.218 ---
obs0.218 30376 96.9 %-
Displacement parametersBiso mean: 15 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.65→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1894 0 2 197 2093
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d24.6
X-RAY DIFFRACTIONx_improper_angle_d0.66
X-RAY DIFFRACTIONx_mcbond_it1.061.5
X-RAY DIFFRACTIONx_mcangle_it1.622
X-RAY DIFFRACTIONx_scbond_it2.172
X-RAY DIFFRACTIONx_scangle_it3.262.5
LS refinement shellResolution: 1.65→1.71 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.285 133 4.8 %
Rwork0.334 2618 -
obs--89 %
Software
*PLUS
Name: X-PLOR(ONLINE) / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.66
X-RAY DIFFRACTIONx_mcbond_it1.061.5
X-RAY DIFFRACTIONx_scbond_it2.172
X-RAY DIFFRACTIONx_mcangle_it1.622
X-RAY DIFFRACTIONx_scangle_it3.262.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.285 / % reflection Rfree: 4.8 % / Rfactor Rwork: 0.334

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