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- PDB-1qmf: PENICILLIN-BINDING PROTEIN 2X (PBP-2X) ACYL-ENZYME COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1qmf
TitlePENICILLIN-BINDING PROTEIN 2X (PBP-2X) ACYL-ENZYME COMPLEX
ComponentsPENICILLIN-BINDING PROTEIN 2X
KeywordsCELL CYCLE / PEPTIDOGLYCAN SYNTHESIS / CELL WALL
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
Chem-CES / CEFUROXIME (OCT-3-ENE FORM) / Penicillin-binding protein 2x
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 1.1Apr 17, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / 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 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)77,6163
Polymers76,8081
Non-polymers8082
Water1,02757
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)129.910, 129.910, 139.860
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
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH CEFUROXIME ANTIBIOTIC / Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Gene: PBP2X / Plasmid: PGEX / Production host: ESCHERICHIA COLI MC1061 (bacteria) / References: UniProt: P14677
#2: Chemical ChemComp-CES / 2-[CARBOXY-(2-FURAN-2-YL-2-METHOXYIMINO-ACETYLAMINO)-METHYL]-5-METHYL-3,6-DIHYDRO-2H-[1,3]THIAZINE-4-CARBOXYLIC ACID / CEFUROXIME (INHIBITION FORM)


Mass: 383.376 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17N3O7S
#3: Chemical ChemComp-KEF / CEFUROXIME (OCT-3-ENE FORM) / (6R,7R)-3-CARBAMOYLOXYMETHYL-7-[2-(2-FURYL)-2-(METHOXYIMINO)ACETAMIDO]-8-OXO-5-THIA-1-AZABICYCLO[4.2.0]OCT-3-ENE-2-CARB OXYLIC ACID / (6R,7R)-3-CARBAMOYLOXYMETHYL-7-[2-(2-FURYL)-2-(METHOXYIMINO)ACETAMIDO] CEPH-3-EM-4-CARBOXYLIC ACID


Mass: 424.385 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H16N4O8S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.8→50 Å / Num. obs: 29276 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.092
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 0.508 / % possible all: 92
Reflection shell
*PLUS
Highest resolution: 2.8 Å / % possible obs: 92.2 %

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Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALAdata scaling
CNS0.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: APO ENZYME

Resolution: 2.8→50 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2313146.29 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
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
Rfree0.271 2916 10 %RANDOM
Rwork0.239 ---
obs0.239 29276 97.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 20.1677 Å2 / ksol: 0.317581 e/Å3
Displacement parametersBiso mean: 52.4 Å2
Baniso -1Baniso -2Baniso -3
1-10.236 Å20 Å20 Å2
2--10.236 Å20 Å2
3----20.472 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4262 0 54 57 4373
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.63
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.731.5
X-RAY DIFFRACTIONc_mcangle_it4.212
X-RAY DIFFRACTIONc_scbond_it4.372
X-RAY DIFFRACTIONc_scangle_it5.792.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.38 462 10.2 %
Rwork0.341 4067 -
obs--92.2 %
Xplor file
Refine-IDSerial noTopol fileParam file
X-RAY DIFFRACTION1PROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.TOPBOTH_8OCT99.PAR
X-RAY DIFFRACTION3ION.TOPPROTEIN.PARAM
X-RAY DIFFRACTION4BOTH_8OCT99.TOPWATER_REP.PARAM
X-RAY DIFFRACTION5ION.PARAM
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.63
LS refinement shell
*PLUS
Rfactor Rfree: 0.38 / Rfactor obs: 0.341

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