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- PDB-3upo: Structure of penicillin-binding protein A from M. tuberculosis: p... -

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Basic information

Database: PDB / ID: 3upo
TitleStructure of penicillin-binding protein A from M. tuberculosis: penicillin G acyl-enzyme complex
ComponentsPenicillin-binding protein A
KeywordsPenicillin-binding protein/Antibiotic / TRANSPEPTIDASE / peptidoglycan peptide / beta-lactam / Penicillin-binding protein-Antibiotic complex
Function / homology
Function and homology information

peptidoglycan L,D-transpeptidase activity / serine-type D-Ala-D-Ala carboxypeptidase / serine-type D-Ala-D-Ala carboxypeptidase activity / penicillin binding / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / plasma membrane => GO:0005886 / membrane => GO:0016020 / plasma membrane / cytosol
Similarity search - Function
Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein 2a (Domain 2) / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
OPEN FORM - PENICILLIN G / Peptidoglycan D,D-transpeptidase PbpA / Peptidoglycan D,D-transpeptidase PbpA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (unknown)
AuthorsDavies, C. / Fedorovich, A.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: The role of the beta5-alpha11 loop in the active-site dynamics of acylated penicillin-binding protein A from Mycobacterium tuberculosis
Authors: Fedarovich, A. / Nicholas, R.A. / Davies, C.
DepositionNov 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release

Structure visualization

Structure viewerMolecule:

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

Theoretical massNumber of molelcules
Total (without water)97,6024
A: Penicillin-binding protein A
hetero molecules

Theoretical massNumber of molelcules
Total (without water)48,8012
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
B: Penicillin-binding protein A
hetero molecules

Theoretical massNumber of molelcules
Total (without water)48,8012
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.210, 123.210, 97.320
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61


#1: Protein Penicillin-binding protein A / PBPA

Mass: 48464.492 Da / Num. of mol.: 2 / Fragment: UNP residues 35-491 / Mutation: G384R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (unknown) / Strain: H37Rv / Gene: MT0019, MTCY10H4.16c, pbpA, Rv0016c / Plasmid: pT7HTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P71586, UniProt: P9WKD1*PLUS, serine-type D-Ala-D-Ala carboxypeptidase
#2: Chemical ChemComp-PNM / OPEN FORM - PENICILLIN G / Benzylpenicillin

Mass: 336.406 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H20N2O4S / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water / Water

Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

Experimental details


ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.07 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG 3350, 0.2 M NaCl, 0.1 M Bis-Tris pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 8, 2009
RadiationMonochromator: SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→44.3 Å / Num. all: 36564 / Num. obs: 36564 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 34
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 2.7 / % possible all: 91.1


SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3LO7
Resolution: 2.3→44.28 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / SU B: 16.457 / SU ML: 0.187 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.405 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24326 1882 5.1 %RANDOM
Rwork0.19483 ---
obs0.19734 34680 98.03 %-
all-36562 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.642 Å2
Baniso -1Baniso -2Baniso -3
1--0.95 Å2-0.47 Å20 Å2
2---0.95 Å20 Å2
3---1.42 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6464 0 46 48 6558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226656
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3451.9819100
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3925874
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63823.372261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.12715979
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5461556
X-RAY DIFFRACTIONr_chiral_restr0.0860.21043
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025136
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.22941
X-RAY DIFFRACTIONr_nbtor_refined0.2970.24615
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2233
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.286
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2210.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5461.54479
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.9227019
X-RAY DIFFRACTIONr_scbond_it1.48532426
X-RAY DIFFRACTIONr_scangle_it2.494.52081
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 137 -
Rwork0.254 2320 -
obs--90.26 %

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