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- PDB-2c6w: PENICILLIN-BINDING PROTEIN 1A (PBP-1A) FROM STREPTOCOCCUS PNEUMONIAE -

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Basic information

Entry
Database: PDB / ID: 2c6w
TitlePENICILLIN-BINDING PROTEIN 1A (PBP-1A) FROM STREPTOCOCCUS PNEUMONIAE
Components(PENICILLIN-BINDING PROTEIN 1A) x 2
KeywordsPEPTIDOGLYCAN SYNTHESIS / CELL WALL / PENICILLIN-BINDING / ANTIBIOTIC RESISTANCE / CELL SHAPE / MULTIFUNCTIONAL ENZYME
Function / homology
Function and homology information


peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / proteolysis / extracellular region
Similarity search - Function
Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / Transglycosylase / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Lysozyme-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Penicillin-binding protein 1A
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsContreras-Martel, C. / Job, V. / Di Guilmi, A.-M. / Vernet, T. / Dideberg, O. / Dessen, A.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of Penicillin-Binding Protein 1A (Pbp1A) Reveals a Mutational Hotspot Implicated in Beta-Lactam Resistance in Streptococcus Pneumoniae.
Authors: Contreras-Martel, C. / Job, V. / Di Guilmi, A.-M. / Vernet, T. / Dideberg, O. / Dessen, A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structural Studies of the Transpeptidase Domain of Pbp1A from Streptococcus Pneumoniae
Authors: Job, V. / Di Guilmi, A.-M. / Martin, L. / Vernet, T. / Dideberg, O. / Dessen, A.
#2: Journal: J.Bacteriol. / Year: 1998
Title: Identification, Purification, and Charactherization of Transpeptidase and Glycosyltransferase Domains of Streptococcus Pneumoniae Penicillin-Binding Protein 1A
Authors: Di Guilmi, A.-M. / Mouz, N. / Andrieu, J.-P. / Hoskins, J. / Jaskunas, S.R. / Gagnon, J. / Dideberg, O. / Vernet, T.
History
DepositionNov 14, 2005Deposition 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 1.3Dec 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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 / _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: PENICILLIN-BINDING PROTEIN 1A
B: PENICILLIN-BINDING PROTEIN 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2429
Polymers44,9042
Non-polymers3387
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)109.782, 187.256, 51.303
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsPBP-1A IS A MONOMER IN SOLUTION, BUT SINCE IN THIS ENTRYTHERE IS A CLEAVED PEPTIDE FROM THE SAME PROTEIN (CHAIN A)ASSOCIATED WITH THE TRANSPEPTIDASE DOMAIN OFPBP-1A (CHAIN B), THE ENTRY IS MARKED AS DIMERIC.

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Components

#1: Protein/peptide PENICILLIN-BINDING PROTEIN 1A / PBP-1A / EXPORTED PROTEIN 2


Mass: 1825.027 Da / Num. of mol.: 1 / Fragment: GLYCOSYLTRANSFERASE DOMAIN, RESIDUES 51-66
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: R6 / Plasmid: PJAH143 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): MC1061 / References: UniProt: Q8DR59
#2: Protein PENICILLIN-BINDING PROTEIN 1A / PBP-1A / EXPORTED PROTEIN 2


Mass: 43078.492 Da / Num. of mol.: 1 / Fragment: TRANSPEPTIDASE DOMAIN, RESIDUES 267-650
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: R6 / Plasmid: PJAH143 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): MC1061 / References: UniProt: Q8DR59
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCELL WALL FORMATION
Sequence detailsEXTRA PEPTIDE FROM THE GLYLOSYLTRANSFERASE DOMAIN, RESIDUES 51-66. THE SEQUENCE IN THE SEQRES ...EXTRA PEPTIDE FROM THE GLYLOSYLTRANSFERASE DOMAIN, RESIDUES 51-66. THE SEQUENCE IN THE SEQRES RECORDS BELOW IS THE OBSERVED SEQUENCE AND THAT REPORTED BY A.-M.DI GUILMI ET AL.

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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: 3.03 Å3/Da / Density % sol: 57.79 %
Crystal growpH: 7
Details: 13% PEG1000, 50MM NACL, 5MM ZNSO4, 50MM TRIS PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.964
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 24, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.964 Å / Relative weight: 1
ReflectionResolution: 2.61→50 Å / Num. obs: 15084 / % possible obs: 91.9 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 72.7 Å2 / Rsym value: 0.08 / Net I/σ(I): 10.2
Reflection shellResolution: 2.61→2.77 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.3 / % possible all: 72.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C5W

2c5w


Resolution: 2.61→44.99 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 3749779.78 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.276 779 4.9 %RANDOM
Rwork0.24 ---
obs0.24 15917 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.5283 Å2 / ksol: 0.349369 e/Å3
Displacement parametersBiso mean: 68.5 Å2
Baniso -1Baniso -2Baniso -3
1--13.5 Å20 Å20 Å2
2---21.92 Å20 Å2
3---35.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.68 Å0.62 Å
Refinement stepCycle: LAST / Resolution: 2.61→44.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3125 0 7 35 3167
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.691.5
X-RAY DIFFRACTIONc_mcangle_it4.432
X-RAY DIFFRACTIONc_scbond_it3.782
X-RAY DIFFRACTIONc_scangle_it5.492.5
LS refinement shellResolution: 2.61→2.77 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.451 100 4.3 %
Rwork0.411 2228 -
obs--85.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER.PARAMWATER.TOP

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