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- PDB-5e31: 2.3 Angstrom Crystal Structure of the Monomeric Form of Penicilli... -

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Basic information

Entry
Database: PDB / ID: 5.0E+31
Title2.3 Angstrom Crystal Structure of the Monomeric 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 / 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 2 prime
Similarity search - Component
Biological speciesEnterococcus faecium DO (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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: 2.3 Angstrom Crystal Structure of the Monomeric 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
DepositionOct 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Penicillin binding protein 2 prime


Theoretical massNumber of molelcules
Total (without water)70,7611
Polymers70,7611
Non-polymers00
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area29690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.440, 64.340, 182.786
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Penicillin binding protein 2 prime


Mass: 70760.672 Da / Num. of mol.: 1 / Fragment: UNP residues 35-678
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium DO (bacteria) / Gene: pbp5, HMPREF0351_11456 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q3XZN6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein: 13.9 mg/ml, 0.5M Sodium chloride, 0.01M Tris-HCL (pH 8.3), 5mM Penicillin V; Screen: Classics II (H7), 0.15M DL-Malic acid (pH 7.0), 20% (w/v) PEG 3350.

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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: Aug 24, 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: 2.3→29.12 Å / Num. obs: 33135 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 22.4
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
BLU-MAXdata collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DVY

5dvy


Resolution: 2.3→29.12 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.925 / SU B: 13.204 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.329 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24445 1677 5.1 %RANDOM
Rwork0.19676 ---
obs0.19925 30970 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.23 Å2
Baniso -1Baniso -2Baniso -3
1--1.47 Å20 Å20 Å2
2---3.71 Å20 Å2
3---5.18 Å2
Refinement stepCycle: 1 / Resolution: 2.3→29.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4898 0 0 243 5141
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.025022
X-RAY DIFFRACTIONr_bond_other_d0.0010.024767
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.9816799
X-RAY DIFFRACTIONr_angle_other_deg0.751311057
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.8255652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11526.933225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.36215866
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.6191511
X-RAY DIFFRACTIONr_chiral_restr0.090.2765
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_it2.6162.7382593
X-RAY DIFFRACTIONr_mcbond_other2.6172.7382592
X-RAY DIFFRACTIONr_mcangle_it4.1534.0993250
X-RAY DIFFRACTIONr_mcangle_other4.1534.0993251
X-RAY DIFFRACTIONr_scbond_it3.0133.1132429
X-RAY DIFFRACTIONr_scbond_other3.0123.1132429
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8224.5083549
X-RAY DIFFRACTIONr_long_range_B_refined7.35122.25852
X-RAY DIFFRACTIONr_long_range_B_other7.3422.0515789
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 117 -
Rwork0.242 2217 -
obs--97.78 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.8406-1.92390.15223.0382-0.62131.2752-0.1191-0.19810.51860.05780.0873-0.414-0.40690.12610.03180.2746-0.03570.00290.283-0.01070.076745.5634-31.9043-2.9749
23.4522-2.90212.76652.4588-2.38752.4825-0.0772-0.3726-0.37750.10190.26070.2921-0.0927-0.0735-0.18350.25580.0352-0.01720.28310.11870.103116.3896-31.6928-8.9818
36.5956-2.7263-2.71811.1291.10291.47530.0316-0.13190.0988-0.00380.0534-0.0419-0.0880.1663-0.08510.04670.00630.00930.09310.0020.152928.2913-35.3556-34.2336
41.4906-1.8625-0.0183.8131-0.96610.6604-0.0723-0.12430.23720.2438-0.016-0.4541-0.1010.11040.08830.0696-0.0078-0.05590.0903-0.00080.130119.6058-15.9933-24.4758
50.605-0.00820.03541.685-0.26490.37120.0303-0.0612-0.00150.1075-0.01130.0882-0.0102-0.0129-0.01910.14460.0070.00950.18730.00370.0049-2.83276.8176-29.2959
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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