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- PDB-4aa7: E.coli GlmU in complex with an antibacterial inhibitor -

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Basic information

Entry
Database: PDB / ID: 4aa7
TitleE.coli 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 wall organization / cell morphogenesis / 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 wall organization / cell morphogenesis / regulation of cell shape / magnesium ion binding / identical protein binding / membrane / cytosol
Similarity search - Function
Bifunctional UDP-N-acetylglucosamine pyrophosphorylase/glucosamine-1-phosphate N-acetyltransferase / GlmU, C-terminal LbH domain / : / MobA-like NTP transferase / MobA-like NTP transferase domain / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat / Hexapeptide repeat proteins ...Bifunctional UDP-N-acetylglucosamine pyrophosphorylase/glucosamine-1-phosphate N-acetyltransferase / GlmU, C-terminal LbH domain / : / MobA-like NTP transferase / MobA-like NTP transferase domain / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Nucleotide-diphospho-sugar transferases / Mainly Beta
Similarity search - Domain/homology
Chem-R82 / Bifunctional protein GlmU
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionNov 30, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.2Dec 27, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Dec 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_sheet / 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_sheet.number_strands / _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
B: BIFUNCTIONAL PROTEIN GLMU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5137
Polymers49,4442
Non-polymers1,0695
Water6,630368
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)75,6269
Polymers74,1663
Non-polymers1,4606
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 area14020 Å2
ΔGint-142.9 kcal/mol
Surface area23120 Å2
MethodPISA
2
B: BIFUNCTIONAL PROTEIN GLMU
hetero molecules

B: BIFUNCTIONAL PROTEIN GLMU
hetero molecules

B: BIFUNCTIONAL PROTEIN GLMU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,91412
Polymers74,1663
Non-polymers1,7489
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area13860 Å2
ΔGint-140 kcal/mol
Surface area23060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.713, 80.713, 140.061
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-2074-

HOH

21B-2068-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1, -0.001485, -0.000509), (0.001485, -1, 0.000112), (0.000509, -0.000111, -1)0.01757, 0.0415, 0.01127
2given(0.999999, -0.001485, -0.000509), (-0.001485, -0.999999, 0.000112), (-0.000509, -0.000111, -1)0.01757, 0.0415, 0.01127

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Components

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


Mass: 24722.160 Da / Num. of mol.: 2 / Fragment: RESIDUES 227-456
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12
References: UniProt: P0ACC7, glucosamine-1-phosphate N-acetyltransferase, UDP-N-acetylglucosamine diphosphorylase
#2: Chemical ChemComp-R82 / N-(2,4-dimethoxy-5-{[(2R)-2-methyl-2,3-dihydro-1H-indol-1-yl]sulfonyl}phenyl)acetamide


Mass: 390.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H22N2O5S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsR82: N-2,4-DIMETHOXY-5-(2-METHYLINDOLIN-1-YL)SULFONYL-PHENYLACETAMID

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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: 2.78 Å3/Da / Density % sol: 55.83 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.5
Details: 19-22% (W/V) PEG3350, 100MM PCTP PH 5.5 AND 400MM AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP

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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: Oct 18, 2005 / 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→40.36 Å / Num. obs: 33180 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9
Reflection shellResolution: 2→2.11 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.5 / % possible all: 82

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
d*TREKdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3TWD

3twd


Resolution: 2→40.36 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.847 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.157 / 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
Rfree0.22128 1669 5 %RANDOM
Rwork0.17712 ---
obs0.1794 31492 95.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.523 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.06 Å20 Å2
2---0.11 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 2→40.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3289 0 69 368 3726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193401
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9921.9854615
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0565441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84224140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.23115560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6781528
X-RAY DIFFRACTIONr_chiral_restr0.1330.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212552
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→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 88 -
Rwork0.234 1880 -
obs--77.21 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5838-0.0452-0.02330.84460.19141.6651-0.0019-0.05250.0120.02740.022-0.0134-0.04630.0064-0.020.00280.00120.00330.0060.00530.050833.677-13.4161.043
20.67960.0194-0.04340.87750.26091.9086-0.00510.0371-0.0162-0.03950.0279-0.01960.05920.0113-0.02270.0049-0.0023-0.0040.00620.01160.052533.7313.408-1.147
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B232 - 453
2X-RAY DIFFRACTION2A233 - 453

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