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- PDB-4p0m: Crystal structure of an evolved putative penicillin-binding prote... -

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Basic information

Entry
Database: PDB / ID: 4p0m
TitleCrystal structure of an evolved putative penicillin-binding protein homolog, Rv2911, from Mycobacterium tuberculosis
ComponentsD-alanyl-D-alanine carboxypeptidaseMuramoylpentapeptide carboxypeptidase
KeywordsHYDROLASE / PENICILLIN-BINDING PROTEIN / DD-2 CARBOXYPEPTIDASE / DIRECTED EVOLUTION / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / TB STRUCTURAL GENOMICS CONSORTIUM / TBSGC
Function / homology
Function and homology information


serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity
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 speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsKrieger, I. / Yu, M. / Bursey, E. / Hung, L.-W. / Terwilliger, T.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Plos One / Year: 2014
Title: Subfamily-Specific Adaptations in the Structures of Two Penicillin-Binding Proteins from Mycobacterium tuberculosis.
Authors: Prigozhin, D.M. / Krieger, I.V. / Huizar, J.P. / Mavrici, D. / Waldo, G.S. / Hung, L. / Sacchettini, J.C. / Terwilliger, T.C. / Alber, T.
History
DepositionFeb 21, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionMar 12, 2014ID: 2BCF
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Other
Revision 1.2Jul 30, 2014Group: Database references
Revision 1.3Jan 14, 2015Group: Database references
Revision 1.4Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / refine_hist / symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _symmetry.Int_Tables_number

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-alanyl-D-alanine carboxypeptidase


Theoretical massNumber of molelcules
Total (without water)29,0731
Polymers29,0731
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.126, 75.126, 230.435
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-306-

HOH

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Components

#1: Protein D-alanyl-D-alanine carboxypeptidase / Muramoylpentapeptide carboxypeptidase / Probable penicillin-binding protein DacB2 (D-alanyl-D-alanine carboxypeptidase) (DD-peptidase) (DD- ...Probable penicillin-binding protein DacB2 (D-alanyl-D-alanine carboxypeptidase) (DD-peptidase) (DD-carboxypeptidase) (PBP) (DD-transpeptidase) (Serine-type D-ala-D-ala carboxypeptidase) (D-amino acid hydrolase)


Mass: 29072.504 Da / Num. of mol.: 1 / Fragment: UNP residues 25-291 / Mutation: A113V, T197I, N208D, G289D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: dacB, dacB2, MT2979, Rv2911 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q7D6F2, serine-type D-Ala-D-Ala carboxypeptidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 5000, AMMONIUS SULFATE, SODIUM CHLORIDE, TRIS, CITRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97964 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2005
RadiationMonochromator: DOUBLE-CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97964 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 32821 / % possible obs: 100 % / Redundancy: 14.9 % / Rmerge(I) obs: 0.144 / Rsym value: 0.163 / Net I/av σ(I): 21.6 / Net I/σ(I): 7.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementResolution: 2→43.131 Å / SU ML: 0.19 / σ(F): 1.28 / Phase error: 19.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1987 1670 5.09 %
Rwork0.1726 --
obs0.1739 32821 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→43.131 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1913 0 0 150 2063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071968
X-RAY DIFFRACTIONf_angle_d1.12691
X-RAY DIFFRACTIONf_dihedral_angle_d16.245709
X-RAY DIFFRACTIONf_chiral_restr0.065311
X-RAY DIFFRACTIONf_plane_restr0.022356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05630.2651380.21362496X-RAY DIFFRACTION97
2.0563-2.12260.29771200.19552596X-RAY DIFFRACTION100
2.1226-2.19850.22451490.19112643X-RAY DIFFRACTION100
2.1985-2.28650.23061480.17452582X-RAY DIFFRACTION100
2.2865-2.39060.22471590.17552568X-RAY DIFFRACTION100
2.3906-2.51660.20281310.17082644X-RAY DIFFRACTION100
2.5166-2.67420.26651290.17692603X-RAY DIFFRACTION100
2.6742-2.88070.20341360.16982597X-RAY DIFFRACTION100
2.8807-3.17050.19791390.17642594X-RAY DIFFRACTION100
3.1705-3.62910.19541310.17092624X-RAY DIFFRACTION100
3.6291-4.57140.14371560.14632573X-RAY DIFFRACTION100
4.5714-43.14080.18671340.17922631X-RAY DIFFRACTION100

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