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- PDB-3twd: glmuC1 in complex with an antibacterial inhibitor -

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Basic information

Entry
Database: PDB / ID: 3twd
TitleglmuC1 in complex with an antibacterial inhibitor
ComponentsBifunctional protein glmU
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / acetyl transferase / uridyl transferase / 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 / 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 proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat ...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 proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Nucleotide-diphospho-sugar transferases / Mainly Beta
Similarity search - Domain/homology
Chem-GOB / Bifunctional protein GlmU
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLahiri, S. / Otterbein, L.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: In Vitro Validation of Acetyltransferase Activity of GlmU as an Antibacterial Target in Haemophilus influenzae.
Authors: Buurman, E.T. / Andrews, B. / Gao, N. / Hu, J. / Keating, T.A. / Lahiri, S. / Otterbein, L.R. / Patten, A.D. / Stokes, S.S. / Shapiro, A.B.
History
DepositionSep 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Dec 14, 2011Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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)48,1916
Polymers46,9992
Non-polymers1,1914
Water6,990388
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)72,2869
Polymers70,4993
Non-polymers1,7876
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 area13050 Å2
ΔGint-94 kcal/mol
Surface area23260 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)72,2869
Polymers70,4993
Non-polymers1,7876
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area13490 Å2
ΔGint-92 kcal/mol
Surface area23130 Å2
MethodPISA
3
A: Bifunctional protein glmU
hetero molecules

A: Bifunctional protein glmU
hetero molecules

A: Bifunctional protein glmU
hetero molecules

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)144,57218
Polymers140,9986
Non-polymers3,57412
Water1086
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
crystal symmetry operation4_655-x+1,-y,z+1/21
crystal symmetry operation5_555y,-x+y,z+1/21
crystal symmetry operation6_545x-y,x-1,z+1/21
Buried area29530 Å2
ΔGint-214 kcal/mol
Surface area43390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.526, 80.526, 139.850
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-460-

HOH

21A-478-

HOH

31B-509-

HOH

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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: 23499.652 Da / Num. of mol.: 2 / Fragment: UNP residues 233-452
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: glmU, yieA, b3730, JW3708 / Production host: Escherichia coli (E. coli)
References: UniProt: P0ACC7, UDP-N-acetylglucosamine diphosphorylase, glucosamine-1-phosphate N-acetyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOB / 4-({5-[(4-aminophenyl)(phenyl)sulfamoyl]-2,4-dimethoxyphenyl}amino)-4-oxobutanoic acid


Mass: 499.536 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H25N3O7S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.78 Å3/Da / Density % sol: 55.83 %
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

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→69.84 Å / Observed criterion σ(F): 3 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassificationNB
REFMAC5.3.0034refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→69.84 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 1 / SU B: 6.082 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2173 1945 5 %RANDOM
obs-38936 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 84.8 Å2 / Biso mean: 26.32 Å2 / Biso min: 16.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.9→69.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3294 0 80 388 3762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223514
X-RAY DIFFRACTIONr_bond_other_d0.0020.022298
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.9874778
X-RAY DIFFRACTIONr_angle_other_deg0.86635620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3445462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.61823.803142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.41215584
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3111530
X-RAY DIFFRACTIONr_chiral_restr0.080.2548
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024012
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02676
X-RAY DIFFRACTIONr_nbd_refined0.1950.2678
X-RAY DIFFRACTIONr_nbd_other0.2070.22452
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21753
X-RAY DIFFRACTIONr_nbtor_other0.0790.22026
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2299
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.235
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2910.2148
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.242
X-RAY DIFFRACTIONr_mcbond_it0.841.52323
X-RAY DIFFRACTIONr_mcbond_other0.1991.5946
X-RAY DIFFRACTIONr_mcangle_it1.10223604
X-RAY DIFFRACTIONr_scbond_it2.24731361
X-RAY DIFFRACTIONr_scangle_it3.4474.51174
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 104 -
Rwork0.201 2051 -
all-2155 -
obs--72.88 %
Refinement TLS params.Method: refined / Origin x: 33.8083 Å / Origin y: -0.1358 Å / Origin z: 0.0117 Å
111213212223313233
T-0.028 Å2-0.0004 Å20.0017 Å2--0.0127 Å20.0003 Å2---0.0087 Å2
L0.1017 °20.0032 °20.0055 °2-0.3552 °20.0013 °2--0.0598 °2
S0.0036 Å °-0.0026 Å °-0.0019 Å °0.0032 Å °0.0031 Å °0.0068 Å °0.0021 Å °0.0023 Å °-0.0067 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A232 - 453
2X-RAY DIFFRACTION1B232 - 453
3X-RAY DIFFRACTION1A2
4X-RAY DIFFRACTION1B1
5X-RAY DIFFRACTION1A1
6X-RAY DIFFRACTION1B454

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