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- PDB-7o4a: Crystal structure of Penicillin-Binding Protein 1 (PBP1) from Sta... -

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Basic information

Entry
Database: PDB / ID: 7o4a
TitleCrystal structure of Penicillin-Binding Protein 1 (PBP1) from Staphylococcus aureus in complex with piperacillin
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
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/transpeptidase-like
Similarity search - Domain/homology
Hydrolyzed piperacillin / Penicillin-binding protein 1
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus COL (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.028 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 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 9, 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
AAA: Penicillin-binding protein 1
BBB: Penicillin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,7874
Polymers144,7162
Non-polymers1,0712
Water00
1
AAA: Penicillin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8942
Polymers72,3581
Non-polymers5361
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Penicillin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8942
Polymers72,3581
Non-polymers5361
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)178.688, 178.688, 223.652
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:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 64 - 588 / Label seq-ID: 1 - 525

Dom-IDAuth asym-IDLabel asym-ID
1AAAA
2BBBB

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)
Gene: pbp1, SACOL1194 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2WVW5
#2: Chemical ChemComp-YPP / Hydrolyzed piperacillin / (2R,4S)-2-[(R)-carboxy{[(2R)-2-{[(4-ethyl-2,3-dioxopiperazin-1-yl)carbonyl]amino}-2-phenylacetyl]amino}methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid


Mass: 535.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C23H29N5O8S
Source: (gene. exp.) Staphylococcus aureus subsp. aureus COL (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria) / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 4.66 Å3/Da / Density % sol: 73.6 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: D,L-malic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97925 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 3.028→47.397 Å / Num. obs: 26360 / % possible obs: 95.1 % / Redundancy: 32.1 % / Rmerge(I) obs: 0.328 / Rpim(I) all: 0.058 / Net I/σ(I): 14.3
Reflection shellResolution: 3.028→3.306 Å / Rmerge(I) obs: 2.93 / Num. unique obs: 1318 / Rpim(I) all: 0.468

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Processing

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

5tro


Resolution: 3.028→47.394 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.853 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.181 / SU B: 19.631 / SU ML: 0.339 / Average fsc free: 0.8855 / Average fsc work: 0.9075 / Cross valid method: FREE R-VALUE / ESU R Free: 0.558
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2778 1339 5.08 %
Rwork0.2116 25021 -
all0.215 --
obs-26360 63.303 %
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: 84.766 Å2
Baniso -1Baniso -2Baniso -3
1-0.651 Å20.326 Å20 Å2
2--0.651 Å20 Å2
3----2.113 Å2
Refinement stepCycle: LAST / Resolution: 3.028→47.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7840 0 0 0 7840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0138008
X-RAY DIFFRACTIONr_bond_other_d0.0020.0187629
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.66610776
X-RAY DIFFRACTIONr_angle_other_deg1.1741.60417657
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2485982
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4623.858394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.176151457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3321533
X-RAY DIFFRACTIONr_chiral_restr0.0590.2995
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.029058
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021800
X-RAY DIFFRACTIONr_nbd_refined0.220.21604
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.27587
X-RAY DIFFRACTIONr_nbtor_refined0.1730.23794
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.24188
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2185
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0210.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2070.222
X-RAY DIFFRACTIONr_nbd_other0.3010.281
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.290.21
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0080.21
X-RAY DIFFRACTIONr_mcbond_it7.0068.7643946
X-RAY DIFFRACTIONr_mcbond_other6.9938.7633945
X-RAY DIFFRACTIONr_mcangle_it11.03813.1344922
X-RAY DIFFRACTIONr_mcangle_other11.03813.1364923
X-RAY DIFFRACTIONr_scbond_it6.2839.1324060
X-RAY DIFFRACTIONr_scbond_other6.2839.1344061
X-RAY DIFFRACTIONr_scangle_it10.06213.5035854
X-RAY DIFFRACTIONr_scangle_other10.06113.5055855
X-RAY DIFFRACTIONr_lrange_it14.24898.2468662
X-RAY DIFFRACTIONr_lrange_other14.2598.2628663
X-RAY DIFFRACTIONr_ncsr_local_group_10.130.0514937
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.129960.05008
12BBBX-RAY DIFFRACTIONLocal ncs0.129960.05008
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
3.028-3.1060.30770.2731120.27629990.7980.8313.9680.266
3.106-3.1910.349140.3063620.30829520.8250.78412.73710.282
3.191-3.2830.401250.3126190.31528310.6870.76822.74810.292
3.283-3.3830.408380.2877720.29227700.7550.81229.24190.249
3.383-3.4940.307550.2619350.26427130.8340.86236.4910.228
3.494-3.6150.252590.24410360.24426100.870.88541.9540.205
3.615-3.7510.357590.25311690.25825210.8140.87448.71080.217
3.751-3.9030.273830.24915290.2524450.8660.87365.93050.21
3.903-4.0760.2921010.25319530.25523330.8350.85688.04120.205
4.076-4.2730.3291230.24221280.24722520.8490.87799.95560.187
4.273-4.5020.2521110.220240.20221350.9120.9261000.157
4.502-4.7720.2511040.18219390.18620430.9180.9431000.146
4.772-5.0980.278830.19118360.19419200.9080.93999.94790.155
5.098-5.5010.259850.20817120.2117970.9290.9361000.175
5.501-6.0180.285890.19915720.20316610.9190.9471000.169
6.018-6.7150.269800.17414470.17815270.9310.9541000.152
6.715-7.7280.25830.1712780.17413610.9350.9551000.155
7.728-9.4030.234550.16111240.16411790.9460.971000.158
9.403-13.0430.224470.1889020.199500.9580.9799.89470.185
13.043-47.3940.357380.3095710.3126100.920.92599.83610.305

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