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- PDB-6whp: Structure of Choline kinase from Cryptococcus neoformans var. gru... -

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Basic information

Entry
Database: PDB / ID: 6whp
TitleStructure of Choline kinase from Cryptococcus neoformans var. grubii serotype A
ComponentsCholine kinase
KeywordsTRANSFERASE / SSGCID / Choline kinase / Cryptococcus neoformans / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyCholine/ethanolamine kinase / Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / kinase activity / Protein kinase-like domain superfamily / Alpha-Beta Complex / Alpha Beta / Choline kinase
Function and homology information
Biological speciesCryptococcus neoformans var. grubii serotype A (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Structure of Choline kinase from Cryptococcus neoformans var. grubii serotype A
Authors: Abendroth, J. / Delker, S.L. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionApr 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Choline kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4517
Polymers50,1591
Non-polymers2936
Water2,270126
1
A: Choline kinase
hetero molecules

A: Choline kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,90214
Polymers100,3172
Non-polymers58512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
Buried area6210 Å2
ΔGint-93 kcal/mol
Surface area35450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.500, 129.500, 160.010
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

#1: Protein Choline kinase


Mass: 50158.512 Da / Num. of mol.: 1 / Fragment: CrneC.00459.a.B2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487) (fungus)
Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_04408 / Plasmid: CrneC.00459.a.B2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: J9VWY8
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Microlytic/Anatrace MCSG-1 screen, condition D7: 100mM sodium citrate tribasic / citric acid pH 5.5, 20% (w/V) PEG 3350: CrneC.00459.a.B2.PW38290 at 21.6mg/ml: cryo: 20% EG: tray: 293589d7, puck hek5-8

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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: Aug 18, 2017
RadiationMonochromator: C111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 23840 / % possible obs: 96.6 % / Redundancy: 6.429 % / Biso Wilson estimate: 50.374 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.052 / Χ2: 1.03 / Net I/σ(I): 24.84
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.25-2.316.4020.563.2717680.8710.60898.2
2.31-2.376.3950.4594.0117250.8960.49898
2.37-2.446.4430.3635.0916870.940.39497.9
2.44-2.526.3860.2886.3516130.9560.31397.8
2.52-2.66.4540.2447.5315800.9720.26597.6
2.6-2.696.4290.1919.6415230.980.20797.6
2.69-2.796.4170.14712.4814730.9870.1697.4
2.79-2.96.4360.10916.1514080.9930.11897
2.9-3.036.4520.0919.4113530.9950.09896.7
3.03-3.186.4690.0724.4512890.9970.07696.3
3.18-3.356.4650.05331.2912270.9980.05896.3
3.35-3.566.390.04139.3211550.9990.04495.9
3.56-3.86.4830.03446.311010.9990.03696.2
3.8-4.116.430.02953.6610100.9990.03195.4
4.11-4.56.4940.02559.249260.9990.02795.4
4.5-5.036.4590.02461.498520.9990.02694.7
5.03-5.816.5230.02260.757460.9990.02394.4
5.81-7.126.4230.02162.2263310.02393.4
7.12-10.066.4110.0177049410.01892.5
10.06-505.8270.01770.6227710.01887.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.18rc4refinement
PDB_EXTRACT3.25data extraction
MR-Rosettaphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: top 10 hits from hhpred search: 3MES_B, 3FEG_A, 5FTG_A, 3C5I_D, 4DA5_A, 1NW1_A, 2QG7_D, 4R78_A, 3DXQ_A, 2PPQ_A

Resolution: 2.25→40.98 Å / SU ML: 0.2674 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.7314 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2259 1853 7.77 %0
Rwork0.1812 ---
obs0.1847 23835 96.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 51.17 Å2
Refinement stepCycle: LAST / Resolution: 2.25→40.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3361 0 15 126 3502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713482
X-RAY DIFFRACTIONf_angle_d0.83154767
X-RAY DIFFRACTIONf_chiral_restr0.0513519
X-RAY DIFFRACTIONf_plane_restr0.0065629
X-RAY DIFFRACTIONf_dihedral_angle_d17.64671247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.310.26341590.22751679X-RAY DIFFRACTION98.24
2.31-2.380.29351140.21731717X-RAY DIFFRACTION98.07
2.38-2.460.27221500.21691696X-RAY DIFFRACTION97.88
2.46-2.540.23731050.21171737X-RAY DIFFRACTION97.62
2.54-2.650.30481580.21991684X-RAY DIFFRACTION97.67
2.65-2.770.29021380.22121685X-RAY DIFFRACTION97.33
2.77-2.910.24991480.22411667X-RAY DIFFRACTION97.01
2.91-3.090.28521660.21481673X-RAY DIFFRACTION96.74
3.09-3.330.24371380.20241683X-RAY DIFFRACTION96.15
3.33-3.670.23991610.18431679X-RAY DIFFRACTION96.28
3.67-4.20.18381500.15531678X-RAY DIFFRACTION95.51
4.2-5.290.18561100.13991706X-RAY DIFFRACTION94.78
5.29-40.980.18561560.1631698X-RAY DIFFRACTION92.65
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)
11.679998323870.430508682030.2268747751231.46058940690.1624257483042.89290048506-0.0326427502933-0.144202164775-0.146671900146-0.00660790268024-0.0512925653361-0.1200402127140.403324317203-0.2816487937480.08034151336790.357652422005-0.0355134360602-0.02391265326750.2812115463960.1129567928310.347491644335-2.0685296283128.703527799763.8099917877
22.034322923320.338780968677-0.7312838095991.58731747038-0.8882372236213.64499622016-0.0915042444974-0.428109368460.1883827580150.261915158953-0.0773147929681-0.175139490528-0.463131518380.1443867676610.1710974341090.340179890578-0.0291879014521-0.1000677945080.358043742421-0.04199762910570.3435330055543.2606641132144.267284345386.438999998
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 88 through 248 )88 - 2481 - 160
22chain 'A' and (resid 249 through 518 )249 - 518161 - 430

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