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- PDB-7kr9: Bifunctional enzyme GlmU bound to Zn(II) -

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Basic information

Entry
Database: PDB / ID: 7kr9
TitleBifunctional enzyme GlmU bound to Zn(II)
ComponentsBifunctional protein GlmU
KeywordsTRANSFERASE
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 / 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 / Trimeric LpxA-like superfamily / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
ACETYL COENZYME *A / Bifunctional protein GlmU
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMaher, M.J.
Funding support Australia, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1080784 Australia
National Health and Medical Research Council (NHMRC, Australia)1140554 Australia
Australian Research Council (ARC)FT180100397 Australia
CitationJournal: Cell Rep / Year: 2022
Title: Dysregulation of Streptococcus pneumoniae zinc homeostasis breaks ampicillin resistance in a pneumonia infection model.
Authors: Brazel, E.B. / Tan, A. / Neville, S.L. / Iverson, A.R. / Udagedara, S.R. / Cunningham, B.A. / Sikanyika, M. / De Oliveira, D.M.P. / Keller, B. / Bohlmann, L. / El-Deeb, I.M. / Ganio, K. / ...Authors: Brazel, E.B. / Tan, A. / Neville, S.L. / Iverson, A.R. / Udagedara, S.R. / Cunningham, B.A. / Sikanyika, M. / De Oliveira, D.M.P. / Keller, B. / Bohlmann, L. / El-Deeb, I.M. / Ganio, K. / Eijkelkamp, B.A. / McEwan, A.G. / von Itzstein, M. / Maher, M.J. / Walker, M.J. / Rosch, J.W. / McDevitt, C.A.
History
DepositionNov 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)50,5296
Polymers49,4811
Non-polymers1,0475
Water5,044280
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)151,58618
Polymers148,4443
Non-polymers3,14215
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area18560 Å2
ΔGint-188 kcal/mol
Surface area49720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.872, 92.872, 280.703
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-1902-

CA

21A-2243-

HOH

31A-2247-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Bifunctional protein GlmU


Mass: 49481.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: D39 / NCTC 7466 / Gene: glmU, SPD_0874 / Production host: Escherichia coli (E. coli)
References: UniProt: Q04KU2, UDP-N-acetylglucosamine diphosphorylase, glucosamine-1-phosphate N-acetyltransferase

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Non-polymers , 5 types, 285 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 20 mM Tris-HCL, pH 7.2, 20% (v/v) PEG 400, 50 mM NaCl, 300 mM CaCl2, and 1 mM ZnCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→47 Å / Num. obs: 37206 / % possible obs: 99.9 % / Redundancy: 10.3 % / CC1/2: 0.999 / Net I/σ(I): 18.2
Reflection shellResolution: 1.9→1.94 Å / Num. unique obs: 2319 / CC1/2: 0.943

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0258refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HM8
Resolution: 1.9→46.83 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.034 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22697 1862 5 %RANDOM
Rwork0.18517 ---
obs0.18721 35343 99.92 %-
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 mean: 39.347 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20.39 Å20 Å2
2--0.79 Å20 Å2
3----2.56 Å2
Refinement stepCycle: 1 / Resolution: 1.9→46.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3354 0 60 280 3694
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0133481
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173178
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.6584748
X-RAY DIFFRACTIONr_angle_other_deg1.2891.5847355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0155457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49824.099161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09315543
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5031514
X-RAY DIFFRACTIONr_chiral_restr0.1620.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023954
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02665
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_it1.5863.6511817
X-RAY DIFFRACTIONr_mcbond_other1.5733.6481815
X-RAY DIFFRACTIONr_mcangle_it2.4485.462268
X-RAY DIFFRACTIONr_mcangle_other2.4485.4622269
X-RAY DIFFRACTIONr_scbond_it1.9823.9741664
X-RAY DIFFRACTIONr_scbond_other1.9813.9761665
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.155.8582478
X-RAY DIFFRACTIONr_long_range_B_refined6.46746.323879
X-RAY DIFFRACTIONr_long_range_B_other6.32746.0623824
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 144 -
Rwork0.219 2572 -
obs--99.56 %
Refinement TLS params.Method: refined / Origin x: 5.3274 Å / Origin y: -17.4932 Å / Origin z: -43.1433 Å
111213212223313233
T0.009 Å20.0107 Å20.0092 Å2-0.0171 Å20.0213 Å2--0.0769 Å2
L0.2633 °20.1023 °2-0.1258 °2-0.1002 °2-0.1571 °2--0.4121 °2
S-0.0083 Å °-0.0348 Å °-0.1363 Å °-0.0181 Å °-0.0378 Å °-0.0549 Å °0.0265 Å °0.0631 Å °0.0461 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 229
2X-RAY DIFFRACTION1A230 - 459

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