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- PDB-4kql: Hin GlmU bound to WG578 -

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Basic information

Entry
Database: PDB / ID: 4kql
TitleHin GlmU bound to WG578
ComponentsBifunctional protein GlmU
KeywordsTRANSFERASE / beta helix / cell wall biosynthesis / small molecule fragment
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 / cytoplasm
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 transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) ...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 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 / 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-1SG / Bifunctional protein GlmU
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsDoig, P. / Kazmirski, S.L. / Boriack-Sjodin, P.A.
CitationJournal: Bioorg.Med.Chem. / Year: 2014
Title: Rational design of inhibitors of the bacterial cell wall synthetic enzyme GlmU using virtual screening and lead-hopping.
Authors: Doig, P. / Boriack-Sjodin, P.A. / Dumas, J. / Hu, J. / Itoh, K. / Johnson, K. / Kazmirski, S. / Kinoshita, T. / Kuroda, S. / Sato, T.O. / Sugimoto, K. / Tohyama, K. / Aoi, H. / Wakamatsu, K. / Wang, H.
History
DepositionMay 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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: Bifunctional protein GlmU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,81712
Polymers49,3461
Non-polymers1,47111
Water6,593366
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)152,45136
Polymers148,0383
Non-polymers4,41333
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 area20310 Å2
ΔGint-322 kcal/mol
Surface area51640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.190, 108.190, 327.870
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-507-

MG

21A-508-

MG

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Components

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Protein , 1 types, 1 molecules A

#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: 49346.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: glmU, HI_0642 / Production host: Escherichia coli (E. coli)
References: UniProt: P43889, UDP-N-acetylglucosamine diphosphorylase, glucosamine-1-phosphate N-acetyltransferase

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Non-polymers , 5 types, 377 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-1SG / N-(4-{[3-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-5-methoxybenzoyl]amino}phenyl)pyridine-2-carboxamide


Mass: 457.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H19N5O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 3.74 Å3/Da / Density % sol: 67.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 2.0 M ammonium sulfate, 2% PEG400, 0.1 M MES, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 26, 2010
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.31→38 Å / Num. all: 39269 / Num. obs: 35955 / % possible obs: 91.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 49.4 Å2
Reflection shellResolution: 2.31→2.32 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 4.7 / Num. unique all: 5456 / Rsym value: 0.44 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
BUSTER2.11.5refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→30.63 Å / Cor.coef. Fo:Fc: 0.9328 / Cor.coef. Fo:Fc free: 0.909 / SU R Cruickshank DPI: 0.213 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.229 / SU Rfree Blow DPI: 0.193 / SU Rfree Cruickshank DPI: 0.188 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2359 1660 5.07 %RANDOM
Rwork0.1937 ---
all0.1958 32767 --
obs0.1958 32767 99.63 %-
Displacement parametersBiso mean: 48.31 Å2
Baniso -1Baniso -2Baniso -3
1--6.1053 Å20 Å20 Å2
2---6.1053 Å20 Å2
3---12.2106 Å2
Refine analyzeLuzzati coordinate error obs: 0.281 Å
Refinement stepCycle: LAST / Resolution: 2.31→30.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3414 0 92 366 3872
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1267SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes108HARMONIC2
X-RAY DIFFRACTIONt_gen_planes527HARMONIC5
X-RAY DIFFRACTIONt_it3580HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion472SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4333SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3580HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4858HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion3.35
X-RAY DIFFRACTIONt_other_torsion16.6
LS refinement shellResolution: 2.31→2.39 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2376 144 4.83 %
Rwork0.1957 2838 -
all0.1976 2982 -
obs--99.63 %
Refinement TLS params.Method: refined / Origin x: 55.3569 Å / Origin y: 50.5222 Å / Origin z: 35.3074 Å
111213212223313233
T-0.0391 Å2-0.0118 Å2-0.0206 Å2--0.0333 Å20.0027 Å2---0.0526 Å2
L0.3393 °2-0.2537 °20.2808 °2-0.5068 °2-0.3828 °2--0.7543 °2
S0.0023 Å °0.102 Å °0.0568 Å °-0.054 Å °-0.0591 Å °-0.0208 Å °-0.047 Å °0.053 Å °0.0569 Å °
Refinement TLS groupSelection details: { A|* }

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