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- PDB-2c5w: PENICILLIN-BINDING PROTEIN 1A (PBP-1A) ACYL-ENZYME COMPLEX (CEFOT... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2c5w | |||||||||
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Title | PENICILLIN-BINDING PROTEIN 1A (PBP-1A) ACYL-ENZYME COMPLEX (CEFOTAXIME) FROM STREPTOCOCCUS PNEUMONIAE | |||||||||
![]() | (PENICILLIN-BINDING PROTEIN ...) x 2 | |||||||||
![]() | TRANSFERASE/HYDROLASE / PEPTIDOGLYCAN SYNTHESIS / TRANSFERASE-HYDROLASE COMPLEX / ANTIBIOTIC RESISTANCE / CELL SHAPE / MULTIFUNCTIONAL ENZYME | |||||||||
Function / homology | ![]() 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 / outer membrane-bounded periplasmic space / response to antibiotic ...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 / outer membrane-bounded periplasmic space / response to antibiotic / proteolysis / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Contreras-Martel, C. / Job, V. / Di Guilmi, A.-M. / Vernet, T. / Dideberg, O. / Dessen, A. | |||||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96.7 KB | Display | ![]() |
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PDB format | ![]() | 72.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 775.8 KB | Display | ![]() |
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Full document | ![]() | 783.9 KB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 24.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2c6wC ![]() 2bg4 C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | PBP-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
-PENICILLIN-BINDING PROTEIN ... , 2 types, 2 molecules AB
#1: Protein/peptide | 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.) ![]() ![]() ![]() ![]() |
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#2: Protein | 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.) ![]() ![]() ![]() ![]() |
-Non-polymers , 5 types, 75 molecules 








#3: Chemical | ChemComp-ZN / |
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#4: Chemical | |
#5: Chemical | |
#6: Chemical | ChemComp-CEF / |
#7: Water | ChemComp-HOH / |
-Details
Has protein modification | Y |
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Sequence details | EXTRA PEPTIDE FROM THE GLYLOSYLTRANSFERASE DOMAIN, RESIDUES 51-66. THE SEQUENCE IN THE SEQRES ...EXTRA PEPTIDE FROM THE GLYLOSYLTR |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 60.62 % Description: PARTIAL PHASING INFORMATION FROM DIFFERENT SOURCES WAS DEVISED USING SHARP |
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Crystal grow | pH: 7 / Details: 13% PEG1000,50 MM NACL, 5MM ZNSO4,50MM TRIS PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 1, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 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
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BG4 ![]() 2bg4 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.754 Å2 / ksol: 0.342401 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.55→47.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.55→2.71 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
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Xplor file |
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