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- PDB-1w79: Crystal structure of the DD-transpeptidase-carboxypeptidase from ... -

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Basic information

Entry
Database: PDB / ID: 1w79
TitleCrystal structure of the DD-transpeptidase-carboxypeptidase from Actinomadura R39
ComponentsD-alanyl-D-alanine carboxypeptidaseMuramoylpentapeptide carboxypeptidase
KeywordsHYDROLASE / PENICILLIN-BINDING / PEPTIDOGLYCAN / ACTINOMADURA / TRANSPEPTIDASE / ANTIBIOTIC RESISTANCE
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 / response to antibiotic / proteolysis / extracellular region
Similarity search - Function
D-Ala-D-Ala carboxypeptidase C, peptidase S13 / Peptidase S13, D-Ala-D-Ala carboxypeptidase C / D-Ala-D-Ala carboxypeptidase 3 (S13) family / D-tyrosyl-trna(Tyr) Deacylase; Chain: A; / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / 3-Layer(bba) Sandwich / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-alanyl-D-alanine carboxypeptidase
Similarity search - Component
Biological speciesActinomadura sp. R39 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.8 Å
AuthorsSauvage, E. / Herman, R. / Petrella, S. / Duez, C. / Frere, J.M. / Charlier, P.
Citation
Journal: J. Biol. Chem. / Year: 2005
Title: Crystal structure of the Actinomadura R39 DD-peptidase reveals new domains in penicillin-binding proteins.
Authors: Sauvage, E. / Herman, R. / Petrella, S. / Duez, C. / Bouillenne, F. / Frere, J.M. / Charlier, P.
#1: Journal: Biochem J. / Year: 1992
Title: Primary and Predicted Secondary Structure of the Actinomadura R39 Extracellular Dd-Peptidase, a Penicillin-Binding Protein (Pbp) Related to the Escherichia Coli Pbp4
Authors: Granier, B. / Duez, C. / Lepage, S. / Englbert, S. / Dusart, J. / Dideberg, O. / Van Beeumen, J. / Frere, J.M. / Ghuysen, J.M.
History
DepositionAug 31, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 12, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_name_com / entity_src_gen / pdbx_entity_src_syn / struct_ref
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.pdbx_description / _entity.src_method / _entity_name_com.name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 2.0Dec 26, 2018Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_struct_assembly
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Revision 2.1Oct 16, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status / reflns_shell
Item: _pdbx_database_status.status_code_sf / _reflns_shell.Rmerge_I_obs
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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
B: D-alanyl-D-alanine carboxypeptidase
C: D-alanyl-D-alanine carboxypeptidase
D: D-alanyl-D-alanine carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,58520
Polymers200,3354
Non-polymers1,25016
Water32,0851781
1
A: D-alanyl-D-alanine carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4216
Polymers50,0841
Non-polymers3375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: D-alanyl-D-alanine carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3724
Polymers50,0841
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: D-alanyl-D-alanine carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3724
Polymers50,0841
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: D-alanyl-D-alanine carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4216
Polymers50,0841
Non-polymers3375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.187, 93.369, 107.272
Angle α, β, γ (deg.)90.00, 94.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
D-alanyl-D-alanine carboxypeptidase / Muramoylpentapeptide carboxypeptidase / DD-peptidase / Penicillin-binding protein / PBP


Mass: 50083.812 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinomadura sp. R39 (bacteria) / Gene: dac / Production host: Escherichia coli (E. coli)
References: UniProt: P39045, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1781 / Source method: isolated from a natural source / Formula: H2O
Compound detailsBINDS PENICILLIN AND REMOVES C-TERMINAL D-ALANYL RESIDUES FROM SUGAR-PEPTIDE CELL WALL PRECURSOR

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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: 2.46 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 1, 2001
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→59.7 Å / Num. obs: 187527 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 4.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.8 / % possible all: 95.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: OTHER / Resolution: 1.8→19.95 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2588169.12 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: RESIDUES 467 TO 489 NOT SEEN IN THE DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.24 9327 5 %RANDOM
Rwork0.214 ---
obs0.214 187168 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.1288 Å2 / ksol: 0.381451 e/Å3
Displacement parametersBiso mean: 23.5 Å2
Baniso -1Baniso -2Baniso -3
1--4.72 Å20 Å21.79 Å2
2--5.11 Å20 Å2
3----0.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13394 0 64 1781 15239
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it1.692
X-RAY DIFFRACTIONc_scbond_it1.952
X-RAY DIFFRACTIONc_scangle_it2.72.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 1510 5 %
Rwork0.25 28394 -
obs--94.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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