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- PDB-7o4b: Crystal structure of Penicillin-Binding Protein 1 (PBP1) from Sta... -

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Basic information

Entry
Database: PDB / ID: 7o4b
TitleCrystal structure of Penicillin-Binding Protein 1 (PBP1) from Staphylococcus aureus in complex with penicillin G
ComponentsPenicillin-binding protein 1
KeywordsHYDROLASE / Cell division / antibiotic resistance / peptidoglycan synthesis / transpeptidase
Function / homology
Function and homology information


penicillin binding / cell wall organization / plasma membrane
Similarity search - Function
Alpha-Beta Plaits - #2110 / PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / : / Penicillin-binding protein, transpeptidase ...Alpha-Beta Plaits - #2110 / PASTA domain / PASTA domain / PASTA domain profile. / PASTA / 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 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / OPEN FORM - PENICILLIN G / Penicillin-binding protein 1
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus COL (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.593 Å
AuthorsMartinez Caballero, S. / Hermoso, J.A.
CitationJournal: Comput Struct Biotechnol J / Year: 2021
Title: Integrative structural biology of the penicillin-binding protein-1 from Staphylococcus aureus , an essential component of the divisome machinery.
Authors: Martinez-Caballero, S. / Mahasenan, K.V. / Kim, C. / Molina, R. / Feltzer, R. / Lee, M. / Bouley, R. / Hesek, D. / Fisher, J.F. / Munoz, I.G. / Chang, M. / Mobashery, S. / Hermoso, J.A.
History
DepositionApr 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 2.0Jun 1, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine_ls_restr_ncs / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_strand_id / _entity_poly_seq.mon_id / _pdbx_database_status.pdb_format_compatible / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_validate_torsion.auth_asym_id / _refine_ls_restr_ncs.pdbx_auth_asym_id / _struct_conf.beg_auth_asym_id / _struct_conf.end_auth_asym_id / _struct_mon_prot_cis.auth_asym_id / _struct_mon_prot_cis.pdbx_auth_asym_id_2 / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.pdbx_pdb_strand_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.end_auth_asym_id
Revision 2.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)147,02218
Polymers144,7162
Non-polymers2,30616
Water70339
1
A: Penicillin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,5599
Polymers72,3581
Non-polymers1,2018
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Penicillin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4639
Polymers72,3581
Non-polymers1,1058
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)180.649, 180.649, 223.466
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111AAA64 - 589
2111BBB64 - 589

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Penicillin-binding protein 1


Mass: 72358.016 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus COL (bacteria)
Strain: COL / Gene: pbp1, SACOL1194 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2WVW5
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PNM / OPEN FORM - PENICILLIN G


Mass: 336.406 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20N2O4S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.61 Å3/Da / Density % sol: 65.94 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.593→47.513 Å / Num. obs: 45182 / % possible obs: 96.3 % / Redundancy: 24.7 % / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.03 / Net I/σ(I): 22.1
Reflection shellResolution: 2.593→2.846 Å / Rmerge(I) obs: 2.163 / Num. unique obs: 2260 / Rpim(I) all: 0.42

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TRO

5tro


Resolution: 2.593→47.505 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.903 / SU B: 10.331 / SU ML: 0.209 / Cross valid method: FREE R-VALUE / ESU R: 0.515 / ESU R Free: 0.312
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2415 2318 5.13 %
Rwork0.2048 42863 -
all0.207 --
obs-45181 67.427 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 63.226 Å2
Baniso -1Baniso -2Baniso -3
1--0.084 Å2-0.042 Å2-0 Å2
2---0.084 Å20 Å2
3---0.273 Å2
Refinement stepCycle: LAST / Resolution: 2.593→47.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7755 0 94 39 7888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0138002
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177556
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.65110778
X-RAY DIFFRACTIONr_angle_other_deg1.2081.59217482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0145976
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97823.817393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.416151431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.051532
X-RAY DIFFRACTIONr_chiral_restr0.0650.2987
X-RAY DIFFRACTIONr_chiral_restr_other0.1420.22
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029029
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021799
X-RAY DIFFRACTIONr_nbd_refined0.2070.21494
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.26936
X-RAY DIFFRACTIONr_nbtor_refined0.1690.23758
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.23868
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2136
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0230.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1820.215
X-RAY DIFFRACTIONr_nbd_other0.2150.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.4270.21
X-RAY DIFFRACTIONr_mcbond_it5.6736.4283922
X-RAY DIFFRACTIONr_mcbond_other5.6646.4273921
X-RAY DIFFRACTIONr_mcangle_it8.6239.6344892
X-RAY DIFFRACTIONr_mcangle_other8.6239.6364893
X-RAY DIFFRACTIONr_scbond_it5.8666.894079
X-RAY DIFFRACTIONr_scbond_other5.8256.8754066
X-RAY DIFFRACTIONr_scangle_it9.04310.1025886
X-RAY DIFFRACTIONr_scangle_other9.01910.0855869
X-RAY DIFFRACTIONr_lrange_it11.95772.4338485
X-RAY DIFFRACTIONr_lrange_other11.9672.4448486
X-RAY DIFFRACTIONr_ncsr_local_group_10.1140.0514842
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.114160.05008
12CX-RAY DIFFRACTIONLocal ncs0.114160.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.593-2.660.528180.3682890.37548860.7210.8256.28330.353
2.66-2.7330.371250.3686410.36847150.7720.80114.12510.345
2.733-2.8120.47510.3518090.35746100.7340.79518.65510.323
2.812-2.8980.337500.3311160.3344760.7640.79326.050.291
2.898-2.9930.357920.32216430.32443510.770.78539.87590.282
2.993-3.0970.3021140.31820990.31742180.8070.78752.46560.283
3.097-3.2140.2941460.28227240.28240680.8680.85970.55060.243
3.214-3.3440.291960.26134710.26339510.8640.88992.8120.225
3.344-3.4920.2611760.22735980.22837740.9050.9131000.191
3.492-3.6620.2531930.20534140.20836070.9120.9291000.171
3.662-3.8590.2491820.18732690.1934510.9250.9421000.163
3.859-4.0910.2031740.16431020.16532760.9470.9571000.14
4.091-4.3710.1891560.15529240.15630800.9620.9661000.136
4.371-4.7180.1741530.1427360.14228890.9660.9721000.126
4.718-5.1630.2141350.15925440.16226790.9560.9661000.145
5.163-5.7640.2281110.17723250.1824370.9490.9699.9590.163
5.764-6.640.271070.19720780.20121850.9360.9491000.186
6.64-8.0930.211970.20617680.20718650.9380.9391000.199
8.093-11.2820.255910.21814230.22115140.9390.9461000.222
11.282-47.5050.301510.3258900.3239410.8570.8821000.332

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