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- PDB-2zc3: Penicillin-binding protein 2X (PBP 2X) acyl-enzyme complex (biape... -

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Basic information

Entry
Database: PDB / ID: 2zc3
TitlePenicillin-binding protein 2X (PBP 2X) acyl-enzyme complex (biapenem) from Streptococcus pneumoniae
Components(Penicillin-binding protein ...Penicillin-binding proteins) x 3
KeywordsBIOSYNTHETIC PROTEIN / PEPTIDOGLYCAN SYNTHESIS / CELL WALL / PENICILLIN-BINDING / ANTIBIOTICS / BIAPENEM / 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 cycle / 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 / Penicillin-binding protein, dimerisation domain superfamily ...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-BMG / Penicillin-binding protein 2x / Penicillin-binding protein 2X
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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)149,1639
Polymers148,3626
Non-polymers8013
Water1,47782
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)74,5334
Polymers74,1813
Non-polymers3521
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)74,6305
Polymers74,1813
Non-polymers4482
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)149,1639
Polymers148,3626
Non-polymers8013
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation1_554x,y,z-11
identity operation1_555x,y,z1
Buried area16580 Å2
ΔGint-69.2 kcal/mol
Surface area54660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.789, 171.909, 88.666
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, 85 molecules

#4: Chemical ChemComp-BMG / (4R,5S)-3-(6,7-dihydro-5H-pyrazolo[1,2-a][1,2,4]triazol-4-ium-6-ylsulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-meth yl-4,5-dihydro-1H-pyrrole-2-carboxylate / (4R,5S)-3-(6,7-dihydro-5H-pyrazolo[1,2-a][1,2,4]triazol-4-ium-6-ylthio)-5-((2S,3R)-3-hydroxy-1-oxobutan-2-yl)-4- methyl-4,5-dihydro-1H-pyrrole-2-carboxylate


Mass: 352.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H20N4O4S
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.74 Å3/Da / Density % sol: 55.16 %
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 RAXIS V / Detector: IMAGE PLATE / Date: Mar 16, 2006
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: 2.5→29.51 Å / Num. obs: 53714 / % possible obs: 92.7 % / Redundancy: 5.3 % / Biso Wilson estimate: 52.76 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 18.9
Reflection shellResolution: 2.5→2.58 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 5.5 / % possible all: 90.1

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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: 2.5→29.51 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.893 / SU B: 11.417 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 0.594 / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: Hydrogens have been added in the riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.28126 2691 5 %RANDOM
Rwork0.23452 ---
obs0.2369 50660 93.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.99 Å2
Baniso -1Baniso -2Baniso -3
1-2.86 Å20 Å20 Å2
2---3.53 Å20 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9881 0 53 82 10016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02210111
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.961.96813697
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.25751278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.59325.826448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.657151746
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0891536
X-RAY DIFFRACTIONr_chiral_restr0.0650.21547
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.027614
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.180.24257
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2930.27020
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2331
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1310.270
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0830.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.371.56567
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.662210283
X-RAY DIFFRACTIONr_scbond_it0.60234010
X-RAY DIFFRACTIONr_scangle_it1.0374.53414
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 196 -
Rwork0.305 3837 -
obs--97.04 %

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