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- PDB-1w8y: Crystal structure of the nitrocefin acyl-DD-peptidase from Actino... -

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Basic information

Entry
Database: PDB / ID: 1w8y
TitleCrystal structure of the nitrocefin acyl-DD-peptidase from Actinomadura R39.
ComponentsD-alanyl-D-alanine carboxypeptidase
KeywordsHYDROLASE / PENICILLIN-BINDING / ACTINOMADURA / PEPTIDOGLYCAN / NITROCEFIN
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
Chem-NCF / D-alanyl-D-alanine carboxypeptidase
Similarity search - Component
Biological speciesActinomadura sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSauvage, E. / Herman, R. / Petrella, S. / Duez, C. / Frere, J.M. / Charlier, P.
CitationJournal: 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.
History
DepositionOct 1, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 2.0Sep 15, 2021Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / entity_name_com / entity_src_nat / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity_name_com.name / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _entity_src_nat.pdbx_organism_scientific / _entity_src_nat.strain / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)203,33928
Polymers200,3354
Non-polymers3,00424
Water14,934829
1
A: D-alanyl-D-alanine carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8598
Polymers50,0841
Non-polymers7757
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: D-alanyl-D-alanine carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8106
Polymers50,0841
Non-polymers7275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: D-alanyl-D-alanine carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8106
Polymers50,0841
Non-polymers7275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: D-alanyl-D-alanine carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8598
Polymers50,0841
Non-polymers7757
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.490, 94.360, 107.200
Angle α, β, γ (deg.)90.00, 94.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 50083.812 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Actinomadura sp. (bacteria)
References: UniProt: P39045, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / 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: Chemical
ChemComp-NCF / (2R)-2-{(1R)-2-OXO-1-[(2-THIENYLACETYL)AMINO]ETHYL}-5,6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLIC ACID / NITROCEFIN, open form without dinitrophenyl-ethenyl group / (2R)-2-[(1R)-2-oxo-1-{[(thiophen-2-yl)acetyl]amino}ethyl]-5,6-dihydro-2H-1,3-thiazine-4-carboxylic acid


Mass: 342.391 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H14N2O5S2 / Comment: antibiotic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 829 / 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: 2.59 Å3/Da / Density % sol: 52.13 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 10, 2004 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.4→40.8 Å / Num. obs: 69694 / % possible obs: 86.6 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 42.1 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.5
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.2 / % possible all: 80.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W79

1w79


Resolution: 2.4→19.94 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2181110.69 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MAXIMUM LLKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.277 3524 5.1 %RANDOM
Rwork0.22 ---
obs0.22 69453 86.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.8654 Å2 / ksol: 0.36853 e/Å3
Displacement parametersBiso mean: 43.6 Å2
Baniso -1Baniso -2Baniso -3
1--4.25 Å20 Å28.57 Å2
2--12.34 Å20 Å2
3----8.08 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13394 0 168 829 14391
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_d24.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it2.022
X-RAY DIFFRACTIONc_scbond_it1.792
X-RAY DIFFRACTIONc_scangle_it2.532.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.321 535 5 %
Rwork0.288 10143 -
obs--79.8 %
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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