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- PDB-2zc4: Penicillin-binding protein 2X (PBP 2X) acyl-enzyme complex (tebip... -

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Basic information

Entry
Database: PDB / ID: 2zc4
TitlePenicillin-binding protein 2X (PBP 2X) acyl-enzyme complex (tebipenem) from Streptococcus pneumoniae
Components(Penicillin-binding protein ...) x 3
KeywordsBIOSYNTHETIC PROTEIN / PEPTIDOGLYCAN SYNTHESIS / CELL WALL / PENICILLIN-BINDING / ANTIBIOTICS / TEBIPENEM / Antibiotic resistance / Cell cycle / Cell division / Cell shape / Cell wall biogenesis/degradation / Membrane / Secreted / 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
Alpha-Beta Plaits - #2110 / : / 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 ...Alpha-Beta Plaits - #2110 / : / 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 Plaits / Alpha-Beta Complex / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-TEB / Penicillin-binding protein 2x / Penicillin-binding protein 2X
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsYamada, M. / Watanabe, T. / Takeuchi, Y.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2008
Title: Crystal Structures of Biapenem and Tebipenem Complexed with Penicillin-Binding Proteins 2X and 1A from Streptococcus pneumoniae
Authors: Yamada, M. / Watanabe, T. / Baba, N. / Takeuchi, Y. / Ohsawa, F. / Gomi, S.
History
DepositionNov 2, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_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
B: Penicillin-binding protein 2X
C: Penicillin-binding protein 2X
D: Penicillin-binding protein 2X
E: Penicillin-binding protein 2X
F: Penicillin-binding protein 2X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,2299
Polymers148,3626
Non-polymers8673
Water59433
1
A: Penicillin-binding protein 2X
B: Penicillin-binding protein 2X
C: Penicillin-binding protein 2X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5674
Polymers74,1813
Non-polymers3861
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Penicillin-binding protein 2X
E: Penicillin-binding protein 2X
F: Penicillin-binding protein 2X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6635
Polymers74,1813
Non-polymers4822
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Penicillin-binding protein 2X
B: Penicillin-binding protein 2X
C: Penicillin-binding protein 2X
hetero molecules

D: Penicillin-binding protein 2X
E: Penicillin-binding protein 2X
F: Penicillin-binding protein 2X
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,2299
Polymers148,3626
Non-polymers8673
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation1_554x,y,z-11
identity operation1_555x,y,z1
Buried area16680 Å2
ΔGint-67.6 kcal/mol
Surface area53970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.305, 172.063, 88.805
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Penicillin-binding protein ... , 3 types, 6 molecules ADBECF

#1: Protein Penicillin-binding protein 2X / PBP-2X / PBP2X


Mass: 18473.584 Da / Num. of mol.: 2 / Fragment: UNP residues 71-238
Source method: isolated from a genetically manipulated source
Details: N-terminal domain / Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: pbpX / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: P59676, UniProt: P14677*PLUS
#2: Protein Penicillin-binding protein 2X / PBP-2X / PBP2X


Mass: 42000.016 Da / Num. of mol.: 2 / Fragment: UNP residues 241-625
Source method: isolated from a genetically manipulated source
Details: Transpeptidase domain / Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: pbpX / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: P59676, UniProt: P14677*PLUS
#3: Protein Penicillin-binding protein 2X / PBP-2X / PBP2X


Mass: 13707.433 Da / Num. of mol.: 2 / Fragment: UNP residues 626-750
Source method: isolated from a genetically manipulated source
Details: C-terminal domain / Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: pbpX / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: P59676, UniProt: P14677*PLUS

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Non-polymers , 3 types, 36 molecules

#4: Chemical ChemComp-TEB / (4R,5S)-3-(1-(4,5-dihydrothiazol-2-yl)azetidin-3-ylthio)-5-((2S,3R)-3-hydroxy-1-oxobutan-2-yl)-4-methyl-4,5- dihydro-1H-pyrrole-2-carboxylic acid / Tebipenem (open form)


Mass: 385.502 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H23N3O4S2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10-25% PEG4000, 0.2M ammonium sulfate, 0.1M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 18, 2004
Details: A fixed exit SI double crystal monochromator followed bystandard double crystal monochromator and RH-coated downward-deflection mirror with a typical glancing angle of 3.7MRAD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→29.69 Å / Num. obs: 41099 / % possible obs: 99.7 % / Redundancy: 5.6 % / Biso Wilson estimate: 67.18 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.9 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
BSSdata collection
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z2L

2z2l


Resolution: 2.8→29.69 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.887 / SU B: 15.814 / SU ML: 0.312 / Cross valid method: THROUGHOUT / ESU R Free: 0.392 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27438 2059 5 %RANDOM
Rwork0.22497 ---
obs0.22743 39009 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.66 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å20 Å20 Å2
2---3.06 Å20 Å2
3---1.84 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9698 0 55 33 9786
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0229924
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0111.96813444
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.49951256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.55225.835437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.713151710
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6531536
X-RAY DIFFRACTIONr_chiral_restr0.0680.21522
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027462
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.24508
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.26874
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2368
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.275
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0780.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.431.56414
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.772210111
X-RAY DIFFRACTIONr_scbond_it0.65933921
X-RAY DIFFRACTIONr_scangle_it1.1284.53329
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 164 -
Rwork0.296 2792 -
obs--98.93 %

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