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- PDB-8u55: Crystal structure of Enterococcus faecium EnGen25 Penicillin-bind... -

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Basic information

Entry
Database: PDB / ID: 8u55
TitleCrystal structure of Enterococcus faecium EnGen25 Penicillin-binding protein 5 (PBP5)
ComponentsPenicillin-binding protein 5
KeywordsPEPTIDE BINDING PROTEIN / Penicillin-binding protein
Function / homology
Function and homology information


penicillin binding / response to antibiotic / plasma membrane
Similarity search - Function
NTF2-like N-terminal transpeptidase / NTF2-like N-terminal transpeptidase domain / 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 / NTF2-like domain superfamily / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Penicillin-binding protein 5
Similarity search - Component
Biological speciesEnterococcus faecium EnGen0025 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPemberton, O.A. / Shamoo, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal structure of Enterococcus faecium EnGen25 Penicillin-binding protein 5 (PBP5)
Authors: Pemberton, O.A. / Shamoo, Y.
History
DepositionSep 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Penicillin-binding protein 5


Theoretical massNumber of molelcules
Total (without water)72,4631
Polymers72,4631
Non-polymers00
Water4,810267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.227, 62.227, 372.317
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Penicillin-binding protein 5


Mass: 72462.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium EnGen0025 (bacteria)
Gene: pbp5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: M1RM73
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.48 Å3/Da / Density % sol: 50.46 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.18 M CaCl2, 0.09 M HEPES pH 8.0, 31.5% (v/v) Pentaerythritol ethoxylate (15/4 EO/OH), 0.59 mM Undecyl-beta-D-maltoside

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.127134 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127134 Å / Relative weight: 1
ReflectionResolution: 1.9→74.46 Å / Num. obs: 109767 / % possible obs: 100 % / Redundancy: 25 % / CC1/2: 0.984 / Rmerge(I) obs: 0.338 / Rpim(I) all: 0.069 / Rrim(I) all: 0.345 / Χ2: 1.01 / Net I/σ(I): 9.7
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 26.3 % / Rmerge(I) obs: 0.3257 / Num. unique obs: 3772 / CC1/2: 0.587 / Rpim(I) all: 2.358 / Rrim(I) all: 12.141 / Χ2: 0.98

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158)refinement
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→44 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2737 5630 5.13 %
Rwork0.226 --
obs0.2285 109767 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4754 0 0 267 5021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094838
X-RAY DIFFRACTIONf_angle_d0.9966540
X-RAY DIFFRACTIONf_dihedral_angle_d6.647656
X-RAY DIFFRACTIONf_chiral_restr0.056739
X-RAY DIFFRACTIONf_plane_restr0.008859
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.55811600.46313476X-RAY DIFFRACTION100
1.92-1.940.49281960.4383521X-RAY DIFFRACTION100
1.94-1.970.45591750.42973461X-RAY DIFFRACTION100
1.97-1.990.44122020.39213472X-RAY DIFFRACTION100
1.99-2.020.41061750.36483466X-RAY DIFFRACTION100
2.02-2.050.37762010.35313460X-RAY DIFFRACTION100
2.05-2.080.37131820.33473496X-RAY DIFFRACTION99
2.08-2.110.42391790.30983401X-RAY DIFFRACTION100
2.11-2.140.36571990.30843516X-RAY DIFFRACTION100
2.14-2.170.34131620.29183435X-RAY DIFFRACTION99
2.17-2.210.34331770.29683491X-RAY DIFFRACTION99
2.21-2.250.33061860.27933436X-RAY DIFFRACTION100
2.25-2.30.31932060.273452X-RAY DIFFRACTION100
2.3-2.340.31291960.26713428X-RAY DIFFRACTION100
2.34-2.390.3462430.2763509X-RAY DIFFRACTION100
2.39-2.450.32371850.25763401X-RAY DIFFRACTION100
2.45-2.510.33451460.25773514X-RAY DIFFRACTION100
2.51-2.580.32552080.25243473X-RAY DIFFRACTION100
2.58-2.650.28661740.23693451X-RAY DIFFRACTION100
2.65-2.740.27911920.23433504X-RAY DIFFRACTION100
2.74-2.840.31311760.23623554X-RAY DIFFRACTION100
2.84-2.950.30441840.24873433X-RAY DIFFRACTION100
2.95-3.090.33591810.24343449X-RAY DIFFRACTION100
3.09-3.250.29071700.23143513X-RAY DIFFRACTION100
3.25-3.450.26721860.20933517X-RAY DIFFRACTION100
3.45-3.720.25092220.19753403X-RAY DIFFRACTION100
3.72-4.090.22321900.17653479X-RAY DIFFRACTION100
4.09-4.680.1892010.15663457X-RAY DIFFRACTION100
4.68-5.90.20741850.17283480X-RAY DIFFRACTION100
5.9-440.21631910.18433489X-RAY DIFFRACTION100

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