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- PDB-1qme: PENICILLIN-BINDING PROTEIN 2X (PBP-2X) -

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Basic information

Entry
Database: PDB / ID: 1qme
TitlePENICILLIN-BINDING PROTEIN 2X (PBP-2X)
ComponentsPENICILLIN-BINDING PROTEIN 2X
KeywordsPENICILLIN-BINDING PROTEIN / PEPTIDOGLYCAN SYNTHESIS / RESISTANCE / CELL WALL / TRANSMEMBRANE
Function / homology
Function and homology information


penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / response to antibiotic / plasma membrane
Similarity search - Function
: / PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily ...: / PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Penicillin-binding protein 2x
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGordon, E.J. / Mouz, N. / Duee, E. / Dideberg, O.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: The Crystal Structure of the Penicillin-Binding Protein 2X from Streptococcus Pneumoniae and its Acyl-Enzyme Form: Implication in Drug Resistance.
Authors: Gordon, E.J. / Mouz, N. / Duee, E. / Dideberg, O.
#1: Journal: Nat.Struct.Biol. / Year: 1996
Title: X-Ray Structure of Streptococcus Pneumoniae Pbp2X, a Primary Penicillin Target Enzyme
Authors: Pares, S. / Mouz, N. / Petillot, Y. / Hakenbeck, R. / Dideberg, O.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization of a Genetically Engineered Water-Soluble Primary Penicillin Target Enzyme. The High Molecular Mass Pbp2X of Streptococcus Pneumoniae
Authors: Charlier, P. / Buisson, G. / Dideberg, O. / Wierenga, J. / Keck, W. / Laible, G. / Hakenbeck, R.
History
DepositionSep 28, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2000Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Oct 24, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
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 / 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_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 2X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0964
Polymers76,8081
Non-polymers2883
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)129.910, 129.910, 141.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein PENICILLIN-BINDING PROTEIN 2X / PBP-2X / PBP2X


Mass: 76807.969 Da / Num. of mol.: 1 / Fragment: RESIDUES 49-750
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Gene: PBP2X / Plasmid: PGEX / Production host: ESCHERICHIA COLI MC1061 (bacteria) / References: UniProt: P14677
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O

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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: 3.86 Å3/Da / Density % sol: 68 %
Crystal growpH: 4.5
Details: 0.1M SODIUM ACETATE PH 4.5, 1.0-1.3M AMMONIUM SULFATE
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
210 mMTris1drop
350 mM1dropNaCl
40.1 Msodium acetate1reservoir
51.0-1.3 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1995
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 42234 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063
Reflection shellResolution: 2.4→2.55 Å / Rmerge(I) obs: 0.368 / % possible all: 93.5
Reflection shell
*PLUS
Highest resolution: 2.4 Å / % possible obs: 93.5 %

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Processing

Software
NameVersionClassification
CNS0.3refinement
DENZOdata reduction
SCALAdata scaling
CNS0.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PMD

1pmd


Resolution: 2.4→50 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3273002.6 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED. MEMBRANE ANCHOR HAS BEEN DELETED FROM CONSTRUCT. PROTEIN CRYSTALLISED CORRESPONDS TO RESIDUES 49-750. ALSO, RESIDUES 93-182, 233- 253, 621-631 ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 4261 10.1 %RANDOM
Rwork0.197 ---
obs0.197 42234 99.7 %-
Displacement parametersBiso mean: 39 Å2
Baniso -1Baniso -2Baniso -3
1-3.19 Å20 Å20 Å2
2--3.19 Å20 Å2
3----6.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4256 0 15 360 4631
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.121.5
X-RAY DIFFRACTIONc_mcangle_it3.22
X-RAY DIFFRACTIONc_scbond_it3.782
X-RAY DIFFRACTIONc_scangle_it4.932.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.302 229 9.9 %
Rwork0.246 2084 -
obs--29.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION42XC2XC
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
LS refinement shell
*PLUS
Rfactor obs: 0.246

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