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- PDB-3upp: Structure of penicillin-binding protein A from M. tuberculosis: c... -

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Basic information

Entry
Database: PDB / ID: 3upp
TitleStructure of penicillin-binding protein A from M. tuberculosis: ceftrixaone acyl-enzyme complex
ComponentsPenicillin-binding protein A
KeywordsPenicillin-binding protein/Antibiotic / TRANSPEPTIDASE / peptidoglycan / 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 / 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
CEFOTAXIME, C3' cleaved, open, bound form / Peptidoglycan D,D-transpeptidase PbpA / Peptidoglycan D,D-transpeptidase PbpA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
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.
History
DepositionNov 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 2.0Sep 19, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_radiation / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _diffrn_radiation.pdbx_diffrn_protocol / _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 2.1Sep 13, 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 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)97,7244
Polymers96,9292
Non-polymers7952
Water37821
1
A: Penicillin-binding protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8622
Polymers48,4641
Non-polymers3971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Penicillin-binding protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8622
Polymers48,4641
Non-polymers3971
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.078, 123.078, 101.284
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Penicillin-binding protein A / PBPA


Mass: 48464.492 Da / Num. of mol.: 2 / Fragment: UNP residues 35-491
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / 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-CEF / CEFOTAXIME, C3' cleaved, open, bound form / Cefotaxime


Mass: 397.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H15N5O5S2 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE STARTING ANTIBIOTIC IS CEFTRIAXONE. UPON ACYLATION THIS COMPOUND BECOMES COVALENTLY BOUND TO THE PBP
Sequence detailsTHE MUTATION G384R OCCURED DURING PCR

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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: 2.29 Å3/Da / Density % sol: 46.19 %
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

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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: Jun 12, 2011
RadiationMonochromator: SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→45.7 Å / Num. all: 33749 / Num. obs: 33749 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 34.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 2.2 / % possible all: 89.6

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Processing

Software
NameClassification
SERGUIdata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 3LO7

3lo7


Resolution: 2.4→40.29 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.935 / SU B: 20.76 / SU ML: 0.223 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.531 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24708 1708 5.1 %RANDOM
Rwork0.2006 ---
obs0.20296 32018 98.77 %-
all-33726 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.992 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20.22 Å20 Å2
2--0.45 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6517 0 52 21 6590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226716
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.361.9819181
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.555882
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33823.422263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.2115991
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2851556
X-RAY DIFFRACTIONr_chiral_restr0.0830.21046
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025204
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.23184
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.24669
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2245
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2230.285
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5731.54500
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.99927076
X-RAY DIFFRACTIONr_scbond_it1.44832451
X-RAY DIFFRACTIONr_scangle_it2.4134.52105
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 119 -
Rwork0.256 2144 -
obs--88.88 %

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