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- PDB-8cu9: Crystal Structure of Bifunctional protein GlmU from Klebsiella pn... -

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Basic information

Entry
Database: PDB / ID: 8cu9
TitleCrystal Structure of Bifunctional protein GlmU from Klebsiella pneumoniae subsp. pneumoniae
ComponentsBifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU
KeywordsTRANSFERASE / SSGCID / acyltransferase / multifunctional enzyme / nucleotidyltransferase / structural genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyCITRIC ACID / Bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU
Function and homology information
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: to be published
Title: Crystal Structure of Bifunctional protein GlmU from Klebsiella pneumoniae subsp. pneumoniae
Authors: DeBouver, N.D. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionMay 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 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 UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6264
Polymers50,2061
Non-polymers4203
Water2,306128
1
A: Bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU
hetero molecules

A: Bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU
hetero molecules

A: Bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,87712
Polymers150,6183
Non-polymers1,2599
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area15730 Å2
ΔGint-82 kcal/mol
Surface area50510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.150, 139.150, 139.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU


Mass: 50205.859 Da / Num. of mol.: 1 / Fragment: KlpnC.00150.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Gene: glmU, IM758_25600, KW550_14685, KW551_26820, KW555_12970, KW557_26470, KW558_26490, KW559_26805, KW560_26800, KW563_26020, KW564_26790, KWK18_26790, KWL80_26790, KWY79_26790, KWY86_26245, KWZ53_26265
Plasmid: KlpnC.00150.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8F6ZET2
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.47 Å3/Da / Density % sol: 72.5 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: [[Target: KlpnC.00150.a.B1.PW38985] [crystallization: protein at 25.33 mg/mL was mixed 1:1 (0.2 uL protein and 0.2 uL precipitant) with an opt screen based on JCSG+ E1: 0.1 M sodium ...Details: [[Target: KlpnC.00150.a.B1.PW38985] [crystallization: protein at 25.33 mg/mL was mixed 1:1 (0.2 uL protein and 0.2 uL precipitant) with an opt screen based on JCSG+ E1: 0.1 M sodium cacodylate, pH 6.5, 1.0 M tri-sodium citrate] [Barcode: 323500h2] [pin: hnx6-4] [cryo: 20% Ethylene glycol]

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 11, 2021 / Details: Berillium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.65→49.2 Å / Num. obs: 26243 / % possible obs: 99.4 % / Redundancy: 5.244 % / Biso Wilson estimate: 65.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.053 / Χ2: 0.944 / Net I/σ(I): 21.81 / Num. measured all: 137618 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.65-2.725.3080.6372.8310302194119410.8190.707100
2.72-2.795.2970.4913.6910021189218920.870.544100
2.79-2.875.3040.3534.869675182618240.9380.39199.9
2.87-2.965.3110.2466.699470178617830.9650.27399.8
2.96-3.065.2860.1888.759061171417140.980.208100
3.06-3.175.3090.13811.388924168316810.9880.15399.9
3.17-3.295.2770.10614.698448160116010.9920.117100
3.29-3.425.2660.0818.758094153815370.9960.08999.9
3.42-3.575.2750.06323.287939151115050.9970.0799.6
3.57-3.755.2360.04928.917446142414220.9980.05599.9
3.75-3.955.2350.04331.767120136413600.9980.04899.7
3.95-4.195.2260.03835.576669128212760.9980.04299.5
4.19-4.485.170.03439.56313123112210.9990.03899.2
4.48-4.845.1340.03142.175653110811010.9990.03599.4
4.84-5.35.2190.0341.685423105010390.9990.03499
5.3-5.935.2090.03141.2748969559400.9990.03598.4
5.93-6.845.1780.02942.1543298498360.9990.03298.5
6.84-8.385.1670.02546.4836437247050.9990.02797.4
8.38-11.855.0360.02250.3628005745560.9990.02596.9
11.85-49.24.5050.02548.6913923373090.9980.02891.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.20.1-4487refinement
PDB_EXTRACT3.27data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OI6

2oi6


Resolution: 2.65→49.2 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2043 2009 7.66 %
Rwork0.1688 24230 -
obs0.1715 26239 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.83 Å2 / Biso mean: 73.0274 Å2 / Biso min: 34.04 Å2
Refinement stepCycle: final / Resolution: 2.65→49.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3361 0 27 128 3516
Biso mean--95.9 63.3 -
Num. residues----451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073455
X-RAY DIFFRACTIONf_angle_d0.8814704
X-RAY DIFFRACTIONf_chiral_restr0.055547
X-RAY DIFFRACTIONf_plane_restr0.008629
X-RAY DIFFRACTIONf_dihedral_angle_d14.551250
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.65-2.720.35621300.336217621892100
2.72-2.790.36061590.292716921851100
2.79-2.870.3121580.266617011859100
2.87-2.960.29581460.233717141860100
2.96-3.070.28921360.232617391875100
3.07-3.190.26791270.225117251852100
3.19-3.340.28261440.226217401884100
3.34-3.510.22881460.190217091855100
3.52-3.730.18031510.151917071858100
3.73-4.020.18081520.15517251877100
4.02-4.420.151340.13351739187399
4.43-5.070.14351600.11691741190199
5.07-6.370.21791300.16151746187699
6.38-49.20.1781360.14141790192697
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)
14.1808-1.7309-2.69153.04273.02095.30210.08260.18920.11220.1692-0.1398-0.07090.2268-0.3250.05970.4350.02-0.02570.3955-0.0590.5979-16.731617.815215.7037
24.4895-1.4092-0.15524.67771.84066.119-0.0330.1701-0.27930.3934-0.10750.33030.494-0.19790.13860.3561-0.00170.04770.2921-0.0230.4411-21.277921.613323.9681
34.19021.0122-0.69095.23470.28846.83-0.0554-0.31961.10920.27240.8001-0.74170.11271.6661-0.71520.52130.1047-0.13880.7817-0.19730.7868-2.112527.511632.1113
45.1223-0.98412.42445.99923.25966.45570.4617-0.1170.7383-0.22910.5743-1.1867-0.5971.4388-1.02860.6715-0.09720.12160.9545-0.2760.92620.725432.922629.0588
56.0261-3.5690.6047.15562.62982.469-0.20330.32150.574-0.1013-0.0913-0.2649-0.47420.59230.29650.6148-0.0361-0.04340.5311-0.04680.6164-17.38835.827329.5314
60.6258-1.2707-1.77614.23113.16431.1113-0.235-0.22360.09080.70120.4062-0.41430.30050.3491-0.17960.50760.087-0.0710.4957-0.04690.465-5.694718.821823.8687
72.93160.68720.21562.9275-0.22942.8409-0.11150.0587-0.5948-0.040.10970.66610.5673-0.51720.01770.4369-0.1183-0.01060.42280.01320.6443-12.1453-13.074.9505
82.33410.1698-0.4271.5157-0.19651.9011-0.12210.5999-0.8612-0.5934-0.00660.52560.7547-0.82410.15251.0424-0.4085-0.30021.0735-0.24151.3371-25.3156-25.3161-15.5296
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 12 through 53 )A12 - 53
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 128 )A54 - 128
3X-RAY DIFFRACTION3chain 'A' and (resid 129 through 155 )A129 - 155
4X-RAY DIFFRACTION4chain 'A' and (resid 156 through 180 )A156 - 180
5X-RAY DIFFRACTION5chain 'A' and (resid 181 through 205 )A181 - 205
6X-RAY DIFFRACTION6chain 'A' and (resid 206 through 258 )A206 - 258
7X-RAY DIFFRACTION7chain 'A' and (resid 259 through 390 )A259 - 390
8X-RAY DIFFRACTION8chain 'A' and (resid 391 through 462 )A391 - 462

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