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- PDB-3d3h: Crystal structure of a complex of the peptidoglycan glycosyltrans... -

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Basic information

Entry
Database: PDB / ID: 3d3h
TitleCrystal structure of a complex of the peptidoglycan glycosyltransferase domain from Aquifex aeolicus and neryl moenomycin A
ComponentsPenicillin-insensitive transglycosylase
KeywordsTRANSFERASE/ANTIBIOTIC / peptidoglycan glycosyltransferase / cell wall biosynthesis / antibiotics / penicillin-binding protein / transglycosylase / moenomycin / Antibiotic resistance / Cell shape / Cell wall biogenesis/degradation / Hydrolase / Inner membrane / Membrane / Multifunctional enzyme / Peptidoglycan synthesis / Signal-anchor / Transmembrane / TRANSFERASE-ANTIBIOTIC COMPLEX
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 / response to antibiotic / proteolysis ...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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-M4O / Penicillin-binding protein 1A
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsYuan, Y. / Sliz, P. / Walker, S.
CitationJournal: 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
DepositionMay 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 30, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Penicillin-insensitive transglycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1952
Polymers22,9121
Non-polymers1,2821
Water86548
1
A: Penicillin-insensitive transglycosylase
hetero molecules

A: Penicillin-insensitive transglycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3894
Polymers45,8252
Non-polymers2,5642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area2220 Å2
ΔGint-16.6 kcal/mol
Surface area17870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.939, 100.448, 104.022
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-insensitive transglycosylase / Peptidoglycan TGase


Mass: 22912.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: mrcA, ponA / Plasmid: pET48(b)+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O66874, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-M4O / (2R)-3-{[(S)-{[(2R,3R,4R,5S,6S)-3-{[(2S,3R,4R,5S,6R)-3-(acetylamino)-5-{[(2S,3R,4R,5S,6R)-3-(acetylamino)-5-{[(2R,3R,4S,5R,6S)-6-carbamoyl-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl]oxy}-4-hydroxy-6-methyltetrahydro-2H-pyran-2-yl]oxy}-4-hydroxy-6-({[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}methyl)tetrahydro-2H-pyran-2-yl]oxy}-6-carbamoyl-4-(carbamoyloxy)-5-hydroxy-5-methyltetrahydro-2H-pyran-2-yl]oxy}(hydroxy)phosphoryl]oxy}-2-{[(2Z)-3,7-dimethylocta-2,6-dien-1-yl]oxy}propanoic acid / Neryl Moenomycin A


Mass: 1282.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C49H80N5O32P
#3: Water ChemComp-HOH / water / Water


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

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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: 3.13 Å3/Da / Density % sol: 60.72 %
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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 13, 2007
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.31→50 Å / Num. obs: 12059 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 31.1 Å2 / Rsym value: 0.059
Reflection shellResolution: 2.31→2.39 Å / Rsym value: 0.396 / % possible all: 94.8

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2OQO

2oqo


Resolution: 2.31→28.59 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 102724.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.26 739 6.1 %RANDOM
Rwork0.225 ---
obs0.225 12059 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.9162 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 56.7 Å2
Baniso -1Baniso -2Baniso -3
1--12.75 Å20 Å20 Å2
2---18.32 Å20 Å2
3---31.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.31→28.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1422 0 87 48 1557
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_d19.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.611.5
X-RAY DIFFRACTIONc_mcangle_it2.712
X-RAY DIFFRACTIONc_scbond_it2.282
X-RAY DIFFRACTIONc_scangle_it3.642.5
LS refinement shellResolution: 2.31→2.45 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.343 97 5.7 %
Rwork0.331 1615 -
obs--80.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3moe.parmoe.top

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