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- PDB-2c5w: PENICILLIN-BINDING PROTEIN 1A (PBP-1A) ACYL-ENZYME COMPLEX (CEFOT... -

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Basic information

Entry
Database: PDB / ID: 2c5w
TitlePENICILLIN-BINDING PROTEIN 1A (PBP-1A) ACYL-ENZYME COMPLEX (CEFOTAXIME) FROM STREPTOCOCCUS PNEUMONIAE
Components(PENICILLIN-BINDING PROTEIN ...) x 2
KeywordsTRANSFERASE/HYDROLASE / PEPTIDOGLYCAN SYNTHESIS / TRANSFERASE-HYDROLASE COMPLEX / 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 ...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
CEFOTAXIME, C3' cleaved, open, bound form / Penicillin-binding protein 1A
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 2, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2005Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 2.0Oct 3, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_site_gen
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 / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Dec 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.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_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.pdbx_leaving_atom_flag / _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
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)45,92412
Polymers45,0052
Non-polymers92010
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-126.1 kcal/mol
Surface area16500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.376, 183.373, 54.850
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

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PENICILLIN-BINDING PROTEIN ... , 2 types, 2 molecules AB

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


Mass: 1825.027 Da / Num. of mol.: 1 / Fragment: GLYLOSYLTRANSFERASE 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: 43179.594 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

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Non-polymers , 5 types, 75 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CEF / CEFOTAXIME, C3' cleaved, open, bound form


Mass: 397.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15N5O5S2 / Comment: antibiotic*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
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: 3

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Sample preparation

CrystalDensity Matthews: 3.24 Å3/Da / Density % sol: 60.62 %
Description: PARTIAL PHASING INFORMATION FROM DIFFERENT SOURCES WAS DEVISED USING SHARP
Crystal growpH: 7 / Details: 13% PEG1000,50 MM NACL, 5MM ZNSO4,50MM TRIS PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 16766 / % possible obs: 88.4 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 53 Å2 / Rsym value: 0.06 / Net I/σ(I): 15.09
Reflection shellResolution: 2.55→2.71 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.41 / Rsym value: 0.29 / % possible all: 54.1

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
SHARPphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BG4

2bg4
PDB Unreleased entry


Resolution: 2.55→47.07 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 4488958.94 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.255 839 4.8 %RANDOM
Rwork0.234 ---
obs0.234 17350 92.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.754 Å2 / ksol: 0.342401 e/Å3
Displacement parametersBiso mean: 54.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.16 Å20 Å20 Å2
2---18.94 Å20 Å2
3---15.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.55→47.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3170 0 41 65 3276
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_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.181.5
X-RAY DIFFRACTIONc_mcangle_it3.522
X-RAY DIFFRACTIONc_scbond_it3.252
X-RAY DIFFRACTIONc_scangle_it4.622.5
LS refinement shellResolution: 2.55→2.71 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.388 89 4.8 %
Rwork0.344 1757 -
obs--59.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CEF.PARCEF.TOP
X-RAY DIFFRACTION3EGL_XPLOR.PAREGL_XPLOR.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5WATER.PARAMWATER.TOP

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