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- PDB-2zc6: Penicillin-binding protein 1A (PBP 1A) acyl-enzyme complex (tebip... -

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Basic information

Entry
Database: PDB / ID: 2zc6
TitlePenicillin-binding protein 1A (PBP 1A) acyl-enzyme complex (tebipenem) from Streptococcus pneumoniae
Components(Penicillin-binding protein 1A) x 2
KeywordsBIOSYNTHETIC PROTEIN / PEPTIDOGLYCAN SYNTHESIS / CELL WALL / PENICILLIN-BINDING / ANTIBIOTICS / TEBIPENEM / Antibiotic resistance / Cell shape / Cell wall biogenesis/degradation / Multifunctional enzyme / Secreted
Function / homology
Function and homology information


peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / proteolysis ...peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / proteolysis / extracellular region / membrane
Similarity search - Function
Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / Transglycosylase / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Lysozyme-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-TEB / Penicillin-binding protein 1A / peptidoglycan glycosyltransferase / Penicillin-binding protein 1A
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 1.2Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Penicillin-binding protein 1A
B: Penicillin-binding protein 1A
C: Penicillin-binding protein 1A
D: Penicillin-binding protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,70614
Polymers92,4124
Non-polymers1,29410
Water72140
1
A: Penicillin-binding protein 1A
B: Penicillin-binding protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8537
Polymers46,2062
Non-polymers6475
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-102.2 kcal/mol
Surface area16780 Å2
MethodPISA
2
C: Penicillin-binding protein 1A
D: Penicillin-binding protein 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8537
Polymers46,2062
Non-polymers6475
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-95.8 kcal/mol
Surface area16730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.755, 50.277, 109.535
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein/peptide Penicillin-binding protein 1A / PBP-1A / Exported protein 2


Mass: 2639.935 Da / Num. of mol.: 2 / Fragment: UNP residues 47-70
Source method: isolated from a genetically manipulated source
Details: Transglycosylase domain / Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: pbpA, exp2 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DR59, UniProt: Q04707*PLUS
#2: Protein Penicillin-binding protein 1A


Mass: 43565.953 Da / Num. of mol.: 2 / Fragment: UNP residues 264-653 / Mutation: R545Q
Source method: isolated from a genetically manipulated source
Details: Transpeptidase domain / Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: pbp1a / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q549Y6, UniProt: Q04707*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 55.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 0.004-0.006M ZINC SULFATE, 0.05M MES, pH6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2006
Details: Rotated-inclined double-crystal monochromator, rhodium-coated horizontal mirror
RadiationMonochromator: rotated-inclined double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→29.88 Å / Num. obs: 29074 / % possible obs: 100 % / Redundancy: 4.5 % / Biso Wilson estimate: 56.87 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 7.2
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.364 / Mean I/σ(I) obs: 2.7 / % possible all: 99.6

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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: PDB ENTRY 2C6W

2c6w


Resolution: 2.7→29.88 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.873 / Cross valid method: THROUGHOUT / ESU R: 1.129 / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27099 1473 5.1 %RANDOM
Rwork0.22796 ---
obs0.23019 27562 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2--0.13 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6300 0 58 40 6398
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226506
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0241.9498863
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5195796
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24325.175315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.327151016
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.41520
X-RAY DIFFRACTIONr_chiral_restr0.0730.2956
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025054
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.22846
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.24465
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2214
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1050.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0810.26
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3941.53968
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.7226391
X-RAY DIFFRACTIONr_scbond_it0.60232538
X-RAY DIFFRACTIONr_scangle_it1.0434.52468
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 100 -
Rwork0.325 2001 -
obs--99.48 %

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