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- PDB-5dvy: 2.95 Angstrom Crystal Structure of the Dimeric Form of Penicillin... -

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Basic information

Entry
Database: PDB / ID: 5dvy
Title2.95 Angstrom Crystal Structure of the Dimeric Form of Penicillin Binding Protein 2 Prime from Enterococcus faecium
ComponentsPenicillin binding protein 2 prime
KeywordsPENICILLIN-BINDING PROTEIN / penicillin binding protein 2 prime / PBP2 / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


penicillin binding / response to antibiotic / membrane => GO:0016020 / plasma membrane
Similarity search - Function
NTF2-like N-terminal transpeptidase domain / NTF2-like N-terminal transpeptidase / 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 2 prime
Similarity search - Component
Biological speciesEnterococcus faecium DO (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.95 Å
AuthorsMinasov, G. / Wawrzak, Z. / Shuvalova, L. / Dubrovska, I. / Flores, K. / Filippova, E. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 2.95 Angstrom Crystal Structure of the Dimeric Form of Penicillin Binding Protein 2 Prime from Enterococcus faecium.
Authors: Minasov, G. / Wawrzak, Z. / Shuvalova, L. / Dubrovska, I. / Flores, K. / Filippova, E. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Penicillin binding protein 2 prime
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,50016
Polymers71,0331
Non-polymers1,46715
Water4,378243
1
A: Penicillin binding protein 2 prime
hetero molecules

A: Penicillin binding protein 2 prime
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,00032
Polymers142,0662
Non-polymers2,93430
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
Buried area6400 Å2
ΔGint-299 kcal/mol
Surface area59160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.162, 193.162, 156.478
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Penicillin binding protein 2 prime


Mass: 71032.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium DO (unknown) / Strain: DO / Gene: pbp5, HMPREF0351_11456 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q3XZN6
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 5.82 Å3/Da / Density % sol: 78.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein: 12.4 mg/ml, 0.01M Tris-HCL (pH 8.3), Screen: Classics II (A3), 0.1M Bis-Tris (pH 5.5), 2M Ammonium sulfate, Cryo: 25% Sucrose, 2M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 9, 2015
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.95→30 Å / Num. obs: 36548 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 13.2 % / Biso Wilson estimate: 68.2 Å2 / Rmerge(I) obs: 0.13 / Rsym value: 0.13 / Net I/σ(I): 23.7
Reflection shellResolution: 2.95→3 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
BLU-MAXdata collection
RefinementMethod to determine structure: SAD / Resolution: 2.95→29.91 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 14.762 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.284 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18678 1762 4.8 %RANDOM
Rwork0.1527 ---
obs0.15437 34772 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.06 Å20 Å2
2---0.11 Å20 Å2
3---0.36 Å2
Refinement stepCycle: 1 / Resolution: 2.95→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4898 0 78 243 5219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.025082
X-RAY DIFFRACTIONr_bond_other_d0.0010.024768
X-RAY DIFFRACTIONr_angle_refined_deg1.5151.9956887
X-RAY DIFFRACTIONr_angle_other_deg0.746311056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.0525650
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.64726.974228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.39515864
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9421511
X-RAY DIFFRACTIONr_chiral_restr0.0880.2778
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.025817
X-RAY DIFFRACTIONr_gen_planes_other0.0190.021030
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3273.712589
X-RAY DIFFRACTIONr_mcbond_other2.3263.7062587
X-RAY DIFFRACTIONr_mcangle_it3.7585.5653242
X-RAY DIFFRACTIONr_mcangle_other3.7575.5653243
X-RAY DIFFRACTIONr_scbond_it4.2154.1662493
X-RAY DIFFRACTIONr_scbond_other4.1944.1662493
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9526.0853646
X-RAY DIFFRACTIONr_long_range_B_refined7.91529.7485856
X-RAY DIFFRACTIONr_long_range_B_other7.91529.7645857
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.951→3.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 111 -
Rwork0.242 2453 -
obs--96.32 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.5356-0.3079-0.12774.91220.77253.0363-0.04330.26920.7659-0.2312-0.0181-0.1215-0.70110.07060.06140.40030.10380.1120.29370.02990.251942.0811102.29772.8457
21.2788-2.4633-2.56777.78715.87315.47740.05820.1716-0.19970.1626-0.41530.4061-0.0683-0.4250.35710.06760.08960.01520.2786-0.05020.143936.654773.257567.9767
32.23121.21632.5194.8244-0.78447.27570.0826-0.3001-0.55880.40820.1088-0.2580.7485-0.0373-0.19140.31750.19250.1510.34540.06940.330257.137151.619882.3817
41.2452-1.2039-1.12461.56541.02951.2581-0.0744-0.3204-0.01750.22090.08930.1644-0.02870.1243-0.01490.22230.05750.06240.3928-0.06440.265957.047263.699563.4187
51.2577-0.2187-0.3811.56730.03771.2488-0.04780.0762-0.0918-0.2261-0.10290.22020-0.16290.15070.05380.043-0.03820.1367-0.09560.093761.557154.880632.6142
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 160
2X-RAY DIFFRACTION2A161 - 184
3X-RAY DIFFRACTION2A306 - 345
4X-RAY DIFFRACTION3A185 - 265
5X-RAY DIFFRACTION4A266 - 305
6X-RAY DIFFRACTION4A383 - 412
7X-RAY DIFFRACTION5A346 - 382
8X-RAY DIFFRACTION5A413 - 678

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