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- PDB-2j9p: Crystal structure of the Bacillus subtilis PBP4a, and its complex... -

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Basic information

Entry
Database: PDB / ID: 2j9p
TitleCrystal structure of the Bacillus subtilis PBP4a, and its complex with a peptidoglycan mimetic peptide.
ComponentsD-alanyl-D-alanine carboxypeptidase DacC
KeywordsHYDROLASE / D-ALA-D-ALA- CARBOXYPEPTIDASE / PEPTIDOGLYCAN SYNTHESIS / PENICILLIN-BINDING PROTEIN / PEPTIDOGLYCAN / CELL DIVISION / BACILLUS SUBTILIS / CELL WALL / CELL SHAPE / CELL CYCLE
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 / cell cycle / membrane raft / cell division ...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 / cell cycle / 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-ALANINE / Chem-REZ / D-alanyl-D-alanine carboxypeptidase DacC
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSauvage, E. / Herman, R. / Kerff, F. / Duez, C. / Charlier, P.
CitationJournal: 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.
History
DepositionNov 15, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2007Provider: 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.pdbx_ec / _entity.src_method / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
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 / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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


Theoretical massNumber of molelcules
Total (without water)100,1976
Polymers99,5262
Non-polymers6714
Water0
1
A: D-alanyl-D-alanine carboxypeptidase DacC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0983
Polymers49,7631
Non-polymers3352
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: D-alanyl-D-alanine carboxypeptidase DacC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0983
Polymers49,7631
Non-polymers3352
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)73.859, 77.586, 164.739
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 DacC / DD-peptidase / Penicillin-binding protein 4a / PBP-4a


Mass: 49762.906 Da / Num. of mol.: 2 / Fragment: RESIDUES 30-491
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: dacC, pbp, BSU18350 / Production host: Escherichia coli (E. coli) / Strain (production host): JM110
References: UniProt: P39844, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-REZ / (2R)-2-AMINO-7-{[(1R)-1-CARBOXYETHYL]AMINO}-7-OXOHEPTANOIC ACID


Mass: 246.260 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H18N2O5
#3: Chemical ChemComp-DAL / D-ALANINE / Alanine


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2

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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: 2.42 Å3/Da / Density % sol: 48.77 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→24.6 Å / Num. obs: 21562 / % possible obs: 91 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 11.2
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.4 / % possible all: 93

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W5D

1w5d


Resolution: 2.8→19.9 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1848421.52 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1049 4.9 %RANDOM
Rwork0.208 ---
obs0.208 21499 89.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.1097 Å2 / ksol: 0.354716 e/Å3
Displacement parametersBiso mean: 43.3 Å2
Baniso -1Baniso -2Baniso -3
1--7.67 Å20 Å20 Å2
2--4.89 Å20 Å2
3---2.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6922 0 44 0 6966
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_deg1.4
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_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it2.22
X-RAY DIFFRACTIONc_scbond_it1.762
X-RAY DIFFRACTIONc_scangle_it2.72.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.374 173 4.8 %
Rwork0.297 3461 -
obs--92.1 %
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
X-RAY DIFFRACTION5REZ.PARAMREZ.TOP

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