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- PDB-2oi7: E. coli GlmU- Complex with UDP-GlcNAc, desulpho-CoA and GlcNAc-1-PO4 -

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Basic information

Entry
Database: PDB / ID: 2oi7
TitleE. coli GlmU- Complex with UDP-GlcNAc, desulpho-CoA and GlcNAc-1-PO4
ComponentsBifunctional protein glmU
KeywordsTRANSFERASE / LEFT-HANDED BETA HELIX
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 / 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 / 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
: / DESULFO-COENZYME A / Chem-GN1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / Bifunctional protein GlmU
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsOlsen, L.R. / Vetting, M.W. / Roderick, S.L.
CitationJournal: Protein Sci. / Year: 2007
Title: Structure of the E. coli bifunctional GlmU acetyltransferase active site with substrates and products.
Authors: Olsen, L.R. / Vetting, M.W. / Roderick, S.L.
History
DepositionJan 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional protein glmU
B: Bifunctional protein glmU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,08713
Polymers98,5022
Non-polymers3,58511
Water3,189177
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)152,86215
Polymers147,7533
Non-polymers5,10912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
MethodPQS
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)153,39924
Polymers147,7533
Non-polymers5,64721
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area19220 Å2
ΔGint-152 kcal/mol
Surface area48260 Å2
MethodPISA, PQS
3
A: Bifunctional protein glmU
B: Bifunctional protein glmU
hetero molecules

A: Bifunctional protein glmU
B: Bifunctional protein glmU
hetero molecules

A: Bifunctional protein glmU
B: Bifunctional protein glmU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)306,26139
Polymers295,5056
Non-polymers10,75633
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area46740 Å2
ΔGint-170 kcal/mol
Surface area93570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.969, 102.969, 644.076
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-6003-

CO

21B-6001-

CO

31B-6002-

CO

DetailsThe biological assembly is trimeric. One trimer is assembled by a crystallographic threefold operation on subunit A. A second trimer is assembled by a crystallographic threefold operation on subunit B. The crystallographic threefold rotation is at (x,y) = (1/3,2/3).

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Bifunctional protein glmU


Mass: 49250.906 Da / Num. of mol.: 2 / Fragment: GlmU
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: glmU / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0ACC7, UDP-N-acetylglucosamine diphosphorylase, glucosamine-1-phosphate N-acetyltransferase
#2: Sugar ChemComp-GN1 / 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose / 2-(ACETYLAMINO)-2-DEOXY-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE / N-ACETYL-D-GLUCOSAMINE-1-PHOSPHATE / N-acetyl-1-O-phosphono-alpha-D-glucosamine / 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucose / 2-acetamido-2-deoxy-1-O-phosphono-D-glucose / 2-acetamido-2-deoxy-1-O-phosphono-glucose


Type: D-saccharide / Mass: 301.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H16NO9P
IdentifierTypeProgram
a-D-Glcp1PO3NAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 6 types, 186 molecules

#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-DCA / DESULFO-COENZYME A


Mass: 735.469 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3
#5: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 177 / 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: 3.33 Å3/Da / Density % sol: 63.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Tris, NaCl, DTT, azide, MgCl2, desulpho-CoA, GlcNAc-1-PO4,UDP-GlcNAc, ammonium sulfate, CoCl2 , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 125 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 15, 2001 / Details: Osmic Blue
RadiationMonochromator: Confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.54→27.45 Å / Num. all: 41785 / Num. obs: 41785 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.072
Reflection shellResolution: 2.54→2.63 Å / Rmerge(I) obs: 0.147 / % possible all: 82.1

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Processing

Software
NameVersionClassification
CNS1refinement
CTRdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1HV9

1hv9


Resolution: 2.54→27.45 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 309819.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2057 4.9 %RANDOM
Rwork0.209 ---
obs0.209 41779 94.3 %-
all-41779 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.9777 Å2 / ksol: 0.359088 e/Å3
Displacement parametersBiso mean: 23.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.35 Å25.77 Å20 Å2
2--2.35 Å20 Å2
3----4.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.54→27.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6764 0 219 177 7160
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.54→2.63 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.326 171 4.8 %
Rwork0.254 3415 -
obs--82.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2CNSFILESGLMU:uni.parCNSFILESGLMU:uni.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4water_rep.paramwater.top
X-RAY DIFFRACTION5protein_break.top

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