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- PDB-7o4c: Crystal structure of PASTA domains of the Penicillin-Binding Prot... -

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Basic information

Entry
Database: PDB / ID: 7o4c
TitleCrystal structure of PASTA domains of the Penicillin-Binding Protein 1 (PBP1) from Staphylococcus aureus
ComponentsPenicillin-binding protein 1
KeywordsHYDROLASE / Cell division / antibiotic resistance / peptidoglycan synthesis / transpeptidase / penicillin-binding protein
Function / homology
Function and homology information


penicillin binding / 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
Penicillin-binding protein 1
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus COL (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 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 / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)25,3303
Polymers25,2952
Non-polymers351
Water2,990166
1
A: Penicillin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6832
Polymers12,6471
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Penicillin-binding protein 1


Theoretical massNumber of molelcules
Total (without water)12,6471
Polymers12,6471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.972, 80.562, 90.422
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Penicillin-binding protein 1


Mass: 12647.298 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.88 Å3/Da / Density % sol: 57.26 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: PEG 400 HEPES free acid/sodium hydroxide PEG 3000 Glycerol

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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 PILATUS 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: 1.51→42.51 Å / Num. obs: 46753 / % possible obs: 100 % / Redundancy: 13 % / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.012 / Net I/σ(I): 30.8
Reflection shellResolution: 1.51→1.54 Å / Rmerge(I) obs: 0.687 / Num. unique obs: 2309 / Rpim(I) all: 0.193

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OAU

5oau


Resolution: 1.51→40.31 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.456 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2081 2399 5.1 %RANDOM
Rwork0.1627 ---
obs0.1649 44285 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 169.98 Å2 / Biso mean: 31.602 Å2 / Biso min: 14.79 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å2-0 Å2-0 Å2
2---0.99 Å20 Å2
3----0.06 Å2
Refinement stepCycle: final / Resolution: 1.51→40.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1774 0 1 166 1941
Biso mean--39.64 38.19 -
Num. residues----234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0131907
X-RAY DIFFRACTIONr_bond_other_d0.0180.0171872
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.6332587
X-RAY DIFFRACTIONr_angle_other_deg1.6891.5984376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.425257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.55828.10874
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35915378
X-RAY DIFFRACTIONr_chiral_restr0.0820.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022201
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02355
X-RAY DIFFRACTIONr_rigid_bond_restr14.60133779
LS refinement shellResolution: 1.51→1.549 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 199 -
Rwork0.248 3216 -
all-3415 -
obs--100 %

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