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

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Basic information

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


penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / 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 / Beta-lactamase ...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 / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Alpha-Beta Complex / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-AIX / : / Penicillin-binding protein PbpB
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.407 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 12, 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)60,3295
Polymers59,8011
Non-polymers5284
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-6 kcal/mol
Surface area18650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.246, 84.219, 90.527
Angle α, β, γ (deg.)90.000, 111.310, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-701-

CO

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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-AIX / (2R,4S)-2-[(1R)-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid / AMPICILLIN (open form)


Mass: 351.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H21N3O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 57.4 %
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: 2.407→47.8 Å / Num. obs: 26376 / % possible obs: 99 % / Redundancy: 3.4 % / Net I/σ(I): 10.76
Reflection shellResolution: 2.41→2.49 Å / Num. unique obs: 2587

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.407→47.8 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.22
RfactorNum. reflection% reflection
Rfree0.2498 1312 4.97 %
Rwork0.1969 --
obs0.1996 26373 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 119.32 Å2 / Biso mean: 49.583 Å2 / Biso min: 26.71 Å2
Refinement stepCycle: final / Resolution: 2.407→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3361 0 27 109 3497
Biso mean--55.78 51.09 -
Num. residues----452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0263467
X-RAY DIFFRACTIONf_angle_d0.9174713
X-RAY DIFFRACTIONf_chiral_restr0.054525
X-RAY DIFFRACTIONf_plane_restr0.006642
X-RAY DIFFRACTIONf_dihedral_angle_d11.9812071
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4073-2.50370.3621570.2962270998
2.5037-2.61760.32671260.2632784100
2.6176-2.75560.30081400.2372792100
2.7556-2.92830.28931590.22752771100
2.9283-3.15430.2951400.2152768100
3.1543-3.47160.26321330.18532822100
3.4716-3.97380.21111530.17612778100
3.9738-5.00570.20361450.15972813100
5.0057-47.80.24781590.2017282499

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