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- PDB-6kgh: Crystal structure of Penicillin binding protein 3 (PBP3) from Myc... -

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Basic information

Entry
Database: PDB / ID: 6kgh
TitleCrystal structure of Penicillin binding protein 3 (PBP3) from Mycobacterium tuerculosis (apo-form)
ComponentsPenicillin-binding protein PbpB
KeywordsTRANSFERASE / Penicillin-binding protein / Native form / Mycobacterium tuberculosis
Function / homology
Function and homology information


penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / integral component of plasma membrane
Similarity search - Function
Beta-Lactamase - #330 / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / 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 / DD-peptidase/beta-lactamase superfamily ...Beta-Lactamase - #330 / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / 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 / DD-peptidase/beta-lactamase superfamily / Beta-lactamase / Beta-lactamase/transpeptidase-like / Alpha-Beta Complex / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Penicillin-binding protein PbpB
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.108 Å
AuthorsLu, Z.K. / Zhang, A.L. / Liu, X. / Guddat, L. / Yang, H.T. / Rao, Z.H.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)15 2017YFC0840300 China
Chinese Academy of SciencesXDB08020200 China
National Natural Science Foundation of China81520108019 China
CitationJournal: Mol.Pharmacol. / Year: 2020
Title: Structures ofMycobacterium tuberculosisPenicillin-Binding Protein 3 in Complex with Fivebeta-Lactam Antibiotics Reveal Mechanism of Inactivation.
Authors: Lu, Z. / Wang, H. / Zhang, A. / Liu, X. / Zhou, W. / Yang, C. / Guddat, L. / Yang, H. / Schofield, C.J. / Rao, Z.
History
DepositionJul 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2020Provider: 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 PbpB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0015
Polymers59,8011
Non-polymers2004
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-18 kcal/mol
Surface area18420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.710, 84.220, 90.500
Angle α, β, γ (deg.)90.000, 111.600, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-940-

HOH

21A-943-

HOH

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Components

#1: Protein Penicillin-binding protein PbpB / Penicillin-binding protein 3 / PBP3


Mass: 59801.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: pbpB, ftsI, pbp3, Rv2163c / Plasmid: pGEX-6p-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: L0T911
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.89 Å3/Da / Density % sol: 57.51 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.4 / Details: PEG 3350, CoCl2, MgCl2, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9776 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9776 Å / Relative weight: 1
ReflectionResolution: 2.1→48.1 Å / Num. obs: 39448 / % possible obs: 99 % / Redundancy: 3.5 % / Net I/σ(I): 10.9
Reflection shellResolution: 2.1→2.42 Å / Num. unique obs: 3914

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Aimlessdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.108→48.043 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.63
RfactorNum. reflection% reflection
Rfree0.2218 1945 4.93 %
Rwork0.1891 --
obs0.1907 39448 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.33 Å2 / Biso mean: 37.3379 Å2 / Biso min: 21.61 Å2
Refinement stepCycle: final / Resolution: 2.108→48.043 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3319 0 4 152 3475
Biso mean--56.72 43.02 -
Num. residues----446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0273399
X-RAY DIFFRACTIONf_angle_d0.9114617
X-RAY DIFFRACTIONf_chiral_restr0.063516
X-RAY DIFFRACTIONf_plane_restr0.005623
X-RAY DIFFRACTIONf_dihedral_angle_d11.4982026
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.108-2.16020.26351530.23542671
2.1602-2.21860.27181360.20852675
2.2186-2.28390.24261290.20062625
2.2839-2.35760.24361220.1942664
2.3576-2.44190.25451340.19482673
2.4419-2.53960.21821250.18792686
2.5396-2.65520.24321350.18312695
2.6552-2.79520.18981700.18122642
2.7952-2.97030.27631400.18942660
2.9703-3.19960.25421310.19142699
3.1996-3.52150.21391340.17932690
3.5215-4.03080.16321440.17212684
4.0308-5.07750.19331470.17372694
5.0775-48.0430.2511450.21492745

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