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- PDB-3nb7: Crystal structure of Aquifex Aeolicus Peptidoglycan Glycosyltrans... -

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Basic information

Entry
Database: PDB / ID: 3nb7
TitleCrystal structure of Aquifex Aeolicus Peptidoglycan Glycosyltransferase in complex with Decarboxylated Neryl Moenomycin
ComponentsPenicillin-binding protein 1A
KeywordsTRANSFERASE / Glycosyltransferases / Peptidoglycan Glycosyltransferase / Polysaccharides / cell wall / antibiotics / moenomycin
Function / homology
Function and homology information


peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase 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 / outer membrane-bounded periplasmic space / response to antibiotic ...peptidoglycan glycosyltransferase / peptidoglycan glycosyltransferase 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 / outer membrane-bounded periplasmic space / response to antibiotic / proteolysis / identical protein binding / plasma membrane
Similarity search - Function
Penicillin binding protein transpeptidase fold / Biosynthetic peptidoglycan transglycosylase-like / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / : / Transglycosylase / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like / Lysozyme-like domain superfamily ...Penicillin binding protein transpeptidase fold / Biosynthetic peptidoglycan transglycosylase-like / Glycosyl transferase, family 51 / Penicillin binding protein transglycosylase domain / : / Transglycosylase / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Penicillin-binding protein 1A
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSliz, P. / Yuan, Y. / Walker, S.
Citation
Journal: Acs Chem.Biol. / Year: 2010
Title: Functional and structural analysis of a key region of the cell wall inhibitor moenomycin.
Authors: Fuse, S. / Tsukamoto, H. / Yuan, Y. / Wang, T.S. / Zhang, Y. / Bolla, M. / Walker, S. / Sliz, P. / Kahne, D.
#1: Journal: ACS CHEM.BIOL. / Year: 2008
Title: Structural analysis of the contacts anchoring moenomycin to peptidoglycan glycosyltransferases and implications for antibiotic design
Authors: Yuan, Y. / Fuse, S. / Ostash, B. / Sliz, P. / Kahne, D. / Walker, S.
History
DepositionJun 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1A


Theoretical massNumber of molelcules
Total (without water)22,9121
Polymers22,9121
Non-polymers00
Water00
1
A: Penicillin-binding protein 1A

A: Penicillin-binding protein 1A


Theoretical massNumber of molelcules
Total (without water)45,8252
Polymers45,8252
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area2260 Å2
ΔGint-17 kcal/mol
Surface area17330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.267, 100.493, 102.623
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Penicillin-binding protein 1A / PBP-1a / PBP1a / Penicillin-insensitive transglycosylase / Peptidoglycan TGase / Penicillin- ...PBP-1a / PBP1a / Penicillin-insensitive transglycosylase / Peptidoglycan TGase / Penicillin-sensitive transpeptidase / DD-transpeptidase


Mass: 22912.428 Da / Num. of mol.: 1 / Fragment: UNP residues 59-243
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: vf5 / Gene: aq_624, mrcA, ponA / Plasmid: pET48 b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(De3)
References: UniProt: O66874, Transferases; Glycosyltransferases; Pentosyltransferases
Nonpolymer detailsMETHYLPHOSPHORYL NERYL MOENOMYCIN WAS NOT MODELED IN THE COMPLEX STRUCTURE BECAUSE OF LOW OCCUPANCY

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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: 3.28 Å3/Da / Density % sol: 62.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 MM HEPES, 6% PEG6K, PH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 8408 / % possible obs: 99.2 % / Biso Wilson estimate: 17.4 Å2 / Rsym value: 0.061

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2OQO

2oqo


Resolution: 2.65→25.38 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 125502.46 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED. THE STRUCTURE OF DECARBOXYLATED NERYL MOENOMYCIN IS NOT MODELED IN BECAUSE OF LOW OCCUPANCY, BUT THE ELECTRON DENSITY MAP CLEARLY SHOWS THE DENSITY OF THE LIGAND, ...Details: BULK SOLVENT MODEL USED. THE STRUCTURE OF DECARBOXYLATED NERYL MOENOMYCIN IS NOT MODELED IN BECAUSE OF LOW OCCUPANCY, BUT THE ELECTRON DENSITY MAP CLEARLY SHOWS THE DENSITY OF THE LIGAND, ESPECIALLY THE PHOSPHATE ATOM, IN THE LIGAND BINDING SITE
RfactorNum. reflection% reflectionSelection details
Rfree0.271 500 6.3 %RANDOM
Rwork0.233 ---
obs0.233 7916 93.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.3539 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 74.1 Å2
Baniso -1Baniso -2Baniso -3
1--16.41 Å20 Å20 Å2
2---27.07 Å20 Å2
3---43.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.68 Å
Refinement stepCycle: LAST / Resolution: 2.65→25.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1441 0 0 0 1441
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.432
X-RAY DIFFRACTIONc_scbond_it1.842
X-RAY DIFFRACTIONc_scangle_it2.992.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.65→2.82 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.368 68 6.2 %
Rwork0.4 1032 -
obs--80.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top

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