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- PDB-1w5d: Crystal structure of PBP4a from Bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 1w5d
TitleCrystal structure of PBP4a from Bacillus subtilis
ComponentsPENICILLIN-BINDING PROTEIN
KeywordsHYDROLASE / PENICILLIN-BINDING PROTEIN / D-ALA-D-ALA-CARBOXYPEPTIDASE / PEPTIDOGLYCAN / BACILLUS SUBTILIS / BETA-LACTAM / PEPTIDOGLYCAN SYNTHESIS
Function / homology
Function and homology information


serine-type carboxypeptidase activity / peptidoglycan metabolic process / 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 / membrane raft / cell division / 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 DacC
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSauvage, E. / Herman, R. / Petrella, S. / Duez, C. / Frere, J.M. / Charlier, P.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure of the Bacillus Subtilis Penicillin-Binding Protein 4A, and its Complex with a Peptidoglycan Mimetic Peptide.
Authors: Sauvage, E. / Duez, C. / Herman, R. / Kerff, F. / Petrella, S. / Anderson, J.W. / Adediran, S.A. / Pratt, R.F. / Frere, J.M. / Charlier, P.
#1: Journal: J.Bacteriol. / Year: 2001
Title: Purification and Characterization of Pbp4A, a New Low-Molecular-Weight Penicillin-Binding Protein from Bacillus Subtilis
Authors: Duez, C. / Vanhove, M. / Gallet, X. / Bouillenne, F. / Docquier, J.D. / Brans, A. / Frere, J.M.
History
DepositionAug 6, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PENICILLIN-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8834
Polymers49,7631
Non-polymers1203
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)67.411, 67.411, 228.464
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-1463-

CA

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Components

#1: Protein PENICILLIN-BINDING PROTEIN


Mass: 49762.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BACILLUS SUBTILIS (bacteria)
References: UniProt: P39844, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.93 Å3/Da / Density % sol: 57.7 %
Crystal growpH: 7.8 / Details: TRIS 0.1M, KCL 0.8M, PH 7.8, PEG3350, CACL2 0.2M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976267
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 1, 2001
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976267 Å / Relative weight: 1
ReflectionResolution: 2.1→58.38 Å / Num. obs: 34499 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 4
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.6 / % possible all: 85.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→19.87 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2233933.32 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1705 5 %RANDOM
Rwork0.224 ---
obs0.224 34283 97.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.7461 Å2 / ksol: 0.351299 e/Å3
Displacement parametersBiso mean: 40.8 Å2
Baniso -1Baniso -2Baniso -3
1-5.01 Å23.66 Å20 Å2
2--5.01 Å20 Å2
3----10.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3462 0 3 359 3824
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_d24.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.072
X-RAY DIFFRACTIONc_scbond_it2.252
X-RAY DIFFRACTIONc_scangle_it3.172.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.31 253 5.1 %
Rwork0.273 4727 -
obs--86 %
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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