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- PDB-9mh4: Crystal Structure of Bifunctional protein GlmU from Klebsiella ae... -

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Basic information

Entry
Database: PDB / ID: 9mh4
TitleCrystal Structure of Bifunctional protein GlmU from Klebsiella aerogenes
ComponentsBifunctional protein GlmU
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / GlmU
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 / : / MobA-like NTP transferase / MobA-like NTP transferase domain / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Bifunctional protein GlmU
Similarity search - Component
Biological speciesKlebsiella aerogenes KCTC 2190 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of Bifunctional protein GlmU from Klebsiella aerogenes
Authors: Liu, L. / Cooper, A. / Lovell, S. / Battaile, K.P.
History
DepositionDec 11, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional protein GlmU


Theoretical massNumber of molelcules
Total (without water)50,2401
Polymers50,2401
Non-polymers00
Water00
1
A: Bifunctional protein GlmU

A: Bifunctional protein GlmU

A: Bifunctional protein GlmU


Theoretical massNumber of molelcules
Total (without water)150,7203
Polymers150,7203
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454-z-1/2,-x,y-1/21
crystal symmetry operation10_554-y,z+1/2,-x-1/21
Buried area8850 Å2
ΔGint-35 kcal/mol
Surface area47530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.654, 138.654, 138.654
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Bifunctional protein GlmU


Mass: 50239.980 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella aerogenes KCTC 2190 (bacteria)
Gene: glmU, EAE_07155 / Plasmid: KlaeA.00150.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0H3FLQ9, UDP-N-acetylglucosamine diphosphorylase, glucosamine-1-phosphate N-acetyltransferase
Has protein modificationN

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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: 4.42 Å3/Da / Density % sol: 72.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 30% Tacsimate, 0.1 M sodium cacodylate pH 6.0. KlaeA.00150.a.B1.PW39177 at 15 mg/mL. plate 13557 well A1 drop 1, Puck: PSL0501, Cryo: 100% Tacsimate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Sep 28, 2024
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 3.05→49.02 Å / Num. obs: 17239 / % possible obs: 100 % / Redundancy: 39.8 % / CC1/2: 1 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.025 / Rrim(I) all: 0.157 / Χ2: 1.16 / Net I/σ(I): 28.7 / Num. measured all: 686483
Reflection shellResolution: 3.05→3.13 Å / % possible obs: 100 % / Redundancy: 39.5 % / Rmerge(I) obs: 2.313 / Num. measured all: 50135 / Num. unique obs: 1270 / CC1/2: 0.513 / Rpim(I) all: 0.371 / Rrim(I) all: 2.343 / Χ2: 0.88 / Net I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
PHENIXdev_5438refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→49.02 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2147 831 4.83 %
Rwork0.1801 --
obs0.1818 17217 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.05→49.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3221 0 0 0 3221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043264
X-RAY DIFFRACTIONf_angle_d0.6224423
X-RAY DIFFRACTIONf_dihedral_angle_d12.2541197
X-RAY DIFFRACTIONf_chiral_restr0.046519
X-RAY DIFFRACTIONf_plane_restr0.006583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.240.30391140.27112718X-RAY DIFFRACTION100
3.24-3.490.26341530.20812690X-RAY DIFFRACTION100
3.49-3.840.26181330.21822701X-RAY DIFFRACTION100
3.84-4.40.22091630.16732686X-RAY DIFFRACTION100
4.4-5.540.16851110.15822768X-RAY DIFFRACTION100
5.54-49.020.2011570.16912823X-RAY DIFFRACTION100
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)
10.0376-0.0162-0.04830.1031-0.00220.0528-0.17180.07770.0322-0.23580.23020.3268-0.0102-0.0089-0.00050.6940.07880.01930.77320.02230.9296-52.536518.1785-19.1316
20.0387-0.0063-0.01540.0656-0.01170.019-0.3307-0.189-0.4083-0.44010.116-0.09350.13670.118800.6713-0.0143-0.01990.69760.1250.985-57.85310.6344-12.5594
30.02220.0298-0.03310.0427-0.02190.05410.5568-0.16990.45350.00660.2163-0.0385-0.81720.11990.00040.87210.01470.1940.87290.01240.9257-61.861731.5335-4.8751
40.0959-0.0213-0.09450.0920.09360.13940.1696-0.45840.0579-0.0175-0.2158-0.103-0.12540.4227-0.00010.64850.01390.03120.86190.03090.9222-65.176722.7714-4.4735
50.02410.0322-0.0090.0246-0.00350.0173-0.1057-0.29550.1882-0.07330.09620.14060.14760.139900.57870.091-0.01370.51480.12060.7775-43.048231.6588-20.5837
60.0964-0.13560.00880.5407-0.31040.33330.3316-0.0679-0.9155-0.2365-0.2823-0.73990.09630.3734-0.00590.63920.27370.09630.7893-0.04861.2773-21.676322.4099-29.6102
7-0.0021-0.0009-0.00480.01980.00690.0035-0.06170.0544-0.1738-0.1148-0.1603-0.33480.20040.2473-0.04091.420.68860.43571.5432-0.32322.1834-7.36827.2183-44.6037
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 53 )
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 111 )
3X-RAY DIFFRACTION3chain 'A' and (resid 112 through 180 )
4X-RAY DIFFRACTION4chain 'A' and (resid 181 through 236 )
5X-RAY DIFFRACTION5chain 'A' and (resid 237 through 257 )
6X-RAY DIFFRACTION6chain 'A' and (resid 258 through 390 )
7X-RAY DIFFRACTION7chain 'A' and (resid 391 through 446 )

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