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- PDB-2z2m: Cefditoren-Acylated Penicillin-Binding Protein 2X (PBP2X) from St... -

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Basic information

Entry
Database: PDB / ID: 2z2m
TitleCefditoren-Acylated Penicillin-Binding Protein 2X (PBP2X) from Streptococcus pneumoniae
Components(Penicillin-binding protein ...Penicillin-binding proteins) x 3
KeywordsBIOSYNTHETIC PROTEIN / PEPTIDOGLYCAN SYNTHESIS / CELL WALL / PENICILLIN-BINDING / ANTIBIOTICS / CEFDITOREN
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
Rubrerythrin, domain 2 - #150 / 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 ...Rubrerythrin, domain 2 - #150 / 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 / Rubrerythrin, domain 2 / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Single Sheet / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Alpha-Beta Plaits / Alpha-Beta Complex / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-CDS / Penicillin-binding protein 2x / Penicillin-binding protein 2X
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYamada, M. / Watanabe, T. / Takeuchi, Y.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2007
Title: Crystal Structure of Cefditoren Complexed with Streptococcus pneumoniae Penicillin-Binding Protein 2X: Structural Basis for its High Antimicrobial Activity
Authors: Yamada, M. / Watanabe, T. / Miyara, T. / Baba, N. / Saito, J. / Takeuchi, Y. / Ohsawa, F.
History
DepositionMay 23, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 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
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

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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)149,4759
Polymers148,3626
Non-polymers1,1133
Water1,67593
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)74,7865
Polymers74,1813
Non-polymers6052
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)74,6904
Polymers74,1813
Non-polymers5091
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.735, 171.205, 89.150
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, 96 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CDS / (2R)-2-[(1R)-1-{[(2Z)-2-(2-AMINO-1,3-THIAZOL-4-YL)-2-(METHOXYIMINO)ACETYL]AMINO}-2-OXOETHYL]-5-[(Z)-2-(4-METHYL-1,3-THIAZOL-5-YL)VINYL]-3,6-DIHYDRO-2H-1,3-THIAZINE-4-CARBOXYLIC ACID


Mass: 508.594 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H20N6O5S3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.77 Å3/Da / Density % sol: 55.59 %
Crystal growMethod: vapor diffusion, hanging drop
Details: 10-25% PEG4000, 0.2M ammonium sulfate, 0.1M sodium acetate, VAPOR DIFFUSION, HANGING DROP

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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: Nov 11, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 46229 / % possible obs: 89.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 60.179 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 16.7
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 5.5 / % possible all: 90.5

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Processing

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

2z2l


Resolution: 2.6→29.42 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.898 / SU B: 10.142 / SU ML: 0.22 / Cross valid method: THROUGHOUT / ESU R: 0.805 / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26711 2288 5 %RANDOM
Rwork0.22052 ---
obs0.22279 43896 89.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.402 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2---0.46 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9453 0 71 93 9617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0229692
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9961.9713127
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.21651224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.72625.768423
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.481151660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4321535
X-RAY DIFFRACTIONr_chiral_restr0.0670.21478
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027319
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.180.24211
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.26702
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2350
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4091.56294
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.73329860
X-RAY DIFFRACTIONr_scbond_it0.67933859
X-RAY DIFFRACTIONr_scangle_it1.1444.53267
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 168 -
Rwork0.282 3169 -
obs--90.04 %

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