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- PDB-4ac3: S.pneumoniae GlmU in complex with an antibacterial inhibitor -

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Basic information

Entry
Database: PDB / ID: 4ac3
TitleS.pneumoniae GlmU in complex with an antibacterial inhibitor
ComponentsBIFUNCTIONAL PROTEIN GLMU
KeywordsTRANSFERASE / ACETYL TRANSFERASE / TRANSFERASE-INHIBITOR COMPLEX
Function / homology
Function and homology information


glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process / cell morphogenesis / cell wall organization / regulation of cell shape ...glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process / cell morphogenesis / cell wall organization / regulation of cell shape / magnesium ion binding / membrane / cytoplasm
Similarity search - Function
Bifunctional UDP-N-acetylglucosamine pyrophosphorylase/glucosamine-1-phosphate N-acetyltransferase / GlmU, C-terminal LbH domain / : / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Nucleotidyl transferase domain / Nucleotidyl transferase / Hexapeptide repeat proteins / Hexapeptide repeat ...Bifunctional UDP-N-acetylglucosamine pyrophosphorylase/glucosamine-1-phosphate N-acetyltransferase / GlmU, C-terminal LbH domain / : / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Nucleotidyl transferase domain / Nucleotidyl transferase / Hexapeptide repeat proteins / Hexapeptide repeat / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-R83 / Bifunctional protein GlmU
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsOtterbein, L. / Breed, J. / Ogg, D.J.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2012
Title: Inhibitors of Acetyltransferase Domain of N-Acetylglucosamine-1-Phosphate-Uridyltransferase/ Glucosamine-1-Phosphate-Acetyltransferase (Glmu). Part 1: Hit to Lead Evaluation of a Novel Arylsulfonamide Series.
Authors: Green, O.M. / McKenzie, A.R. / Shapiro, A.B. / Otterbein, L. / Ni, H. / Patten, A. / Stokes, S. / Albert, R. / Kawatkar, S. / Breed, J.
History
DepositionDec 12, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references
Revision 1.2Dec 27, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

Downloads & links

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Assembly

Deposited unit
A: BIFUNCTIONAL PROTEIN GLMU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0253
Polymers49,4811
Non-polymers5442
Water6,702372
1
A: BIFUNCTIONAL PROTEIN GLMU
hetero molecules

A: BIFUNCTIONAL PROTEIN GLMU
hetero molecules

A: BIFUNCTIONAL PROTEIN GLMU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,0759
Polymers148,4443
Non-polymers1,6316
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
Buried area14620 Å2
ΔGint-131.5 kcal/mol
Surface area50840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.090, 117.090, 116.619
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-1461-

SO4

21A-1461-

SO4

31A-2091-

HOH

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Components

#1: Protein BIFUNCTIONAL PROTEIN GLMU / GLCN-1-P ACETYLTRANSFERASE / GLCNAC-1-P URIDYLYLTRANSFERASE / UDP-N-ACETYLGLUCOSAMINE ...GLCN-1-P ACETYLTRANSFERASE / GLCNAC-1-P URIDYLYLTRANSFERASE / UDP-N-ACETYLGLUCOSAMINE PYROPHOSPHORYLASE / N-ACETYLGLUCOSAMINE-1-PHOSPHATE URIDYLTRANSFERASE / GLUCOSAMINE-1-PHOSPHATE N-ACETYLTRANSFERASE


Mass: 49481.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Plasmid: PBA989 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): HMS174 (DE3)
References: UniProt: Q8DQ18, glucosamine-1-phosphate N-acetyltransferase, UDP-N-acetylglucosamine diphosphorylase
#2: Chemical ChemComp-R83 / N-{2,4-DIMETHOXY-5-[(2-PIPERIDIN-1-YLBENZYL)sulfamoyl]phenyl}acetamide


Mass: 447.548 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H29N3O5S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 4.7 Å3/Da / Density % sol: 67 % / Description: NONE
Crystal growpH: 7.5
Details: 18-23% PEG 3350, 0.2M AMMONIUM SULPHATE, 25 MM TRIS-HCL, PH 7.5, 50MM NACL, 2MM TCEP

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU CCD / Detector: CCD / Date: Feb 14, 2006 / Details: RIGAKU VARIMAX HF
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→41.3 Å / Num. obs: 54029 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.1
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.4 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G97

1g97


Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.903 / SU B: 6.902 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.26968 2745 5.1 %RANDOM
Rwork0.23285 ---
obs0.2347 51173 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.025 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3449 0 36 372 3857
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.023538
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0361.964802
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9165454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.24225.455154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.00715594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5151515
X-RAY DIFFRACTIONr_chiral_restr0.1410.2566
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212640
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 197 -
Rwork0.235 3476 -
obs--96.94 %
Refinement TLS params.Method: refined / Origin x: 43.697 Å / Origin y: 44.386 Å / Origin z: 42.426 Å
111213212223313233
T0.0435 Å20.0182 Å2-0.0046 Å2-0.0538 Å20.023 Å2--0.0666 Å2
L0.3288 °2-0.1143 °20.1524 °2-0.0453 °2-0.0532 °2--0.282 °2
S0.0578 Å °0.0728 Å °0.0174 Å °-0.0084 Å °-0.0296 Å °-0.0162 Å °-0.0129 Å °-0.0229 Å °-0.0282 Å °

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