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- PDB-4htl: Lmo2764 protein, a putative N-acetylmannosamine kinase, from List... -

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Basic information

Entry
Database: PDB / ID: 4htl
TitleLmo2764 protein, a putative N-acetylmannosamine kinase, from Listeria monocytogenes
ComponentsBeta-glucoside kinase
KeywordsTRANSFERASE / structural genomics / sugar kinase / ROK family / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


beta-glucoside kinase / beta-glucoside kinase activity / carbohydrate metabolic process / ATP binding
Similarity search - Function
ROK family / ROK family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-glucoside kinase
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.64 Å
AuthorsOsipiuk, J. / Mack, J. / Endres, M. / Salazar, J. / Zhang, W. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Lmo2764 protein, a putative N-acetylmannosamine kinase, from Listeria monocytogenes.
Authors: Osipiuk, J. / Mack, J. / Endres, M. / Salazar, J. / Zhang, W. / Joachimiak, A.
History
DepositionNov 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-glucoside kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8862
Polymers32,8241
Non-polymers621
Water5,693316
1
A: Beta-glucoside kinase
hetero molecules

A: Beta-glucoside kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7724
Polymers65,6482
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area3930 Å2
ΔGint-6 kcal/mol
Surface area23830 Å2
MethodPISA
2
A: Beta-glucoside kinase
hetero molecules

A: Beta-glucoside kinase
hetero molecules

A: Beta-glucoside kinase
hetero molecules

A: Beta-glucoside kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,5448
Polymers131,2964
Non-polymers2484
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area13120 Å2
ΔGint-19 kcal/mol
Surface area42390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.694, 121.989, 153.297
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-402-

HOH

21A-429-

HOH

31A-553-

HOH

Detailsdimer based on PISA

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Components

#1: Protein Beta-glucoside kinase


Mass: 32824.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: bglK, lmo2764 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8Y3R9, beta-glucoside kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 3.12 Å3/Da / Density % sol: 60.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M lithium sulfate, 0.1 M Tris-HCl, 30% PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 4, 2012
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.64→35.9 Å / Num. all: 49631 / Num. obs: 49631 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 32.5 Å2 / Rmerge(I) obs: 0.087 / Χ2: 4.171 / Net I/σ(I): 16.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.64-1.674.80.6052.124030.83196.7
1.67-1.75.70.54624180.85598.3
1.7-1.736.10.47324420.96798.7
1.73-1.776.40.4124481.05198.7
1.77-1.816.80.35424291.20898.9
1.81-1.857.20.30924771.40199.4
1.85-1.897.90.26124491.65299.4
1.89-1.9480.22824691.91199.6
1.94-280.20124982.32299.8
2-2.0780.16924592.806100
2.07-2.148.20.14725153.22599.9
2.14-2.238.10.13524613.781100
2.23-2.338.20.12325064.312100
2.33-2.458.20.11824824.792100
2.45-2.68.10.10524935.428100
2.6-2.880.09625076.199100
2.8-3.0980.08525157.172100
3.09-3.537.70.07225297.958100
3.53-4.457.60.06225438.471100
4.45-507.50.065258812.09198.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.64→36 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.967 / Occupancy max: 1 / Occupancy min: 0.26 / SU B: 2.53 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.073 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1686 2509 5.1 %RANDOM
Rwork0.1277 ---
all0.1298 49630 --
obs0.1298 49630 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.97 Å2 / Biso mean: 29.3068 Å2 / Biso min: 11.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.36 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.64→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2237 0 4 316 2557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022425
X-RAY DIFFRACTIONr_bond_other_d0.0010.021638
X-RAY DIFFRACTIONr_angle_refined_deg1.461.963308
X-RAY DIFFRACTIONr_angle_other_deg0.9834011
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4885328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.59624.138116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13515416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9961515
X-RAY DIFFRACTIONr_chiral_restr0.1040.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022775
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02516
X-RAY DIFFRACTIONr_rigid_bond_restr3.81934063
X-RAY DIFFRACTIONr_sphericity_free35.649590
X-RAY DIFFRACTIONr_sphericity_bonded18.49654222
LS refinement shellResolution: 1.641→1.683 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 170 -
Rwork0.301 3035 -
all-3205 -
obs-3205 90.38 %

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