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- PDB-3upn: Structure of penicillin-binding protein A from M. tuberculosis: i... -

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Basic information

Entry
Database: PDB / ID: 3upn
TitleStructure of penicillin-binding protein A from M. tuberculosis: imipenem 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 / membrane => GO:0016020 / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / plasma membrane / cytosol
Similarity search - Function
: / Penicillin binding protein A dimerisation domain / 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 ...: / Penicillin binding protein A dimerisation domain / 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
Chem-IM2 / Peptidoglycan D,D-transpeptidase PbpA / Peptidoglycan D,D-transpeptidase PbpA
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 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 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)97,5324
Polymers96,9292
Non-polymers6032
Water1,02757
1
A: Penicillin-binding protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7662
Polymers48,4641
Non-polymers3011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Penicillin-binding protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7662
Polymers48,4641
Non-polymers3011
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.800, 122.800, 101.100
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-IM2 / (5R)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-[(2-{[(E)-iminomethyl]amino}ethyl)sulfanyl]-4,5-dihydro-1H-pyrrole-2-carbox ylic acid / IMIPENEM, open form / N-FORMIMIDOYL-THIENAMYCINE, open form


Mass: 301.362 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N3O4S / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE MUTATION AROSE 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: 2.27 Å3/Da / Density % sol: 45.77 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20% PEG 3350, 0.2 M potassium nitrate, pH 5.0, 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: 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: 2.1→46.1 Å / Num. all: 49427 / Num. obs: 49427 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.3 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 37.4
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 7 % / Rmerge(I) obs: 0.638 / Mean I/σ(I) obs: 1.7 / % possible all: 89.3

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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: 2.2→37.35 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 16.164 / SU ML: 0.189 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.315 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25822 2149 4.9 %RANDOM
Rwork0.21421 ---
obs0.21642 41358 99.08 %-
all-49400 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.516 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20.31 Å20 Å2
2--0.62 Å20 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 2.2→37.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6428 0 40 57 6525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226607
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.9819023
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1245866
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.08123.538260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.11215980
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1721554
X-RAY DIFFRACTIONr_chiral_restr0.0830.21034
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025092
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1940.22845
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.24563
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2222
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.275
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6191.54450
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.04726963
X-RAY DIFFRACTIONr_scbond_it1.55532412
X-RAY DIFFRACTIONr_scangle_it2.5644.52060
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 151 -
Rwork0.264 2898 -
obs--95.07 %

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