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- PDB-6c84: Crystal structure of PBP5 from Enterococcus faecium -

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Basic information

Entry
Database: PDB / ID: 6c84
TitleCrystal structure of PBP5 from Enterococcus faecium
ComponentsPenicillin-binding proteinPenicillin-binding proteins
KeywordsMEMBRANE PROTEIN / penicillin binding protein / antibiotic resistance / Peptidoglycan
Function / homology
Function and homology information


penicillin binding / membrane => GO:0016020 / response to antibiotic
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 transpeptidase domain-containing protein
Similarity search - Component
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.511 Å
AuthorsShamoo, Y. / Davlieva, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R22430 United States
CitationJournal: To Be Published
Title: Crystal structure of PBP5 from Enterococcus faecium
Authors: Shamoo, Y. / Davlieva, M.
History
DepositionJan 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Penicillin-binding protein
B: Penicillin-binding protein


Theoretical massNumber of molelcules
Total (without water)143,7142
Polymers143,7142
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint0 kcal/mol
Surface area60610 Å2
Unit cell
Length a, b, c (Å)110.977, 73.071, 131.445
Angle α, β, γ (deg.)90.000, 114.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Penicillin-binding protein / Penicillin-binding proteins / Putative penicillin-binding protein 3


Mass: 71856.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium (bacteria) / Gene: CQR40_00950, HMPREF3199_01318 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A133MY97

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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: 3.36 Å3/Da / Density % sol: 63.41 %
Crystal growMethod: vapor diffusion, hanging drop
Details: 0.2 M Mg acetate, 0.1 M Na cacodylate pH 6.5, 5% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.51→30 Å / Num. obs: 65301 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 42.66 Å2 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.057 / Rrim(I) all: 0.112 / Χ2: 1.33 / Net I/σ(I): 10.4 / Num. measured all: 246829
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.51-2.553.80.82932200.7490.4950.9670.968100
2.55-2.63.80.76432560.7370.4570.8920.981100
2.6-2.653.80.6432390.8170.3820.7461.013100
2.65-2.73.80.54232330.8490.3250.6341.08799.9
2.7-2.763.80.43632540.9020.2610.5091.06100
2.76-2.833.80.36332410.9370.2170.4241.108100
2.83-2.93.80.32432480.9390.1930.3781.135100
2.9-2.983.80.26532360.960.1580.3091.155100
2.98-3.063.80.21832750.9630.130.2541.217100
3.06-3.163.80.16932400.9790.1010.1971.257100
3.16-3.273.80.1432700.9870.0830.1631.287100
3.27-3.413.80.11332470.9870.0670.1321.36100
3.41-3.563.80.09532550.990.0570.1111.525100
3.56-3.753.80.08832830.990.0520.1021.77100
3.75-3.983.80.07432540.9930.0440.0861.83599.9
3.98-4.293.80.06232830.9930.0370.0721.706100
4.29-4.723.80.05632740.9950.0330.0651.66100
4.72-5.43.80.05232820.9950.0310.0611.59799.9
5.4-6.793.70.05133220.9940.030.0591.51199.8
6.79-303.50.0433890.9970.0250.0471.35899.6

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.511→29.79 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 31.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.265 1898 3.05 %
Rwork0.2238 60395 -
obs0.2251 62293 95.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 238.65 Å2 / Biso mean: 82.023 Å2 / Biso min: 29.74 Å2
Refinement stepCycle: final / Resolution: 2.511→29.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9797 0 0 0 9797
Num. residues----1281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069947
X-RAY DIFFRACTIONf_angle_d0.83113454
X-RAY DIFFRACTIONf_chiral_restr0.0491517
X-RAY DIFFRACTIONf_plane_restr0.0051778
X-RAY DIFFRACTIONf_dihedral_angle_d5.5216090
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5112-2.5740.37981120.30423615372781
2.574-2.64350.36881190.28933955407487
2.6435-2.72130.29871250.26814009413489
2.7213-2.80910.33991350.26684147428292
2.8091-2.90940.3051280.26654221434994
2.9094-3.02580.32211360.27174325446196
3.0258-3.16330.37391380.25814388452697
3.1633-3.32990.32491380.25074444458298
3.3299-3.53820.26111430.23674448459199
3.5382-3.81090.25551450.21444535468099
3.8109-4.19340.20511420.192245234665100
4.1934-4.79810.18931430.181545424685100
4.7981-6.03680.24061480.209545794727100
6.0368-29.79180.26541460.207846644810100
Refinement TLS params.Method: refined / Origin x: 154.2717 Å / Origin y: 4.5228 Å / Origin z: 28.8543 Å
111213212223313233
T0.5424 Å2-0.0202 Å20.0411 Å2-0.5885 Å20.0092 Å2--0.4719 Å2
L0.293 °2-0.0146 °20.4059 °2--0.049 °20.0296 °2--0.0263 °2
S0.014 Å °0.1121 Å °-0.0153 Å °-0.0427 Å °-0.0082 Å °-0.0205 Å °-0.0326 Å °0.1135 Å °0.0009 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA39 - 678
2X-RAY DIFFRACTION1allB38 - 678

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