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- PDB-9drz: Structure of Lichtheimia corymbifera Kinase in complex with GDP and MG -

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Basic information

Entry
Database: PDB / ID: 9drz
TitleStructure of Lichtheimia corymbifera Kinase in complex with GDP and MG
Componentsp-loop containing nucleoside triphosphatehydrolase protein
KeywordsMETAL BINDING PROTEIN / kinase
Function / homologyAAA domain / hydrolase activity / P-loop containing nucleoside triphosphate hydrolase / GUANOSINE-5'-DIPHOSPHATE / p-loop containing nucleoside triphosphatehydrolase protein
Function and homology information
Biological speciesLichtheimia corymbifera (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWimberly-Gard, G.M. / Shuman, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM126945 United States
CitationJournal: To Be Published
Title: Structure of Lichtheimia corymbifera Kinase in complex with GDP and MG
Authors: Wimberly-Gard, G.M. / Shuman, S.
History
DepositionSep 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: p-loop containing nucleoside triphosphatehydrolase protein
B: p-loop containing nucleoside triphosphatehydrolase protein
C: p-loop containing nucleoside triphosphatehydrolase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5279
Polymers57,1253
Non-polymers1,4036
Water41423
1
A: p-loop containing nucleoside triphosphatehydrolase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5093
Polymers19,0421
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: p-loop containing nucleoside triphosphatehydrolase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5093
Polymers19,0421
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: p-loop containing nucleoside triphosphatehydrolase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5093
Polymers19,0421
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.469, 120.469, 166.733
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-309-

HOH

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Components

#1: Protein p-loop containing nucleoside triphosphatehydrolase protein


Mass: 19041.643 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lichtheimia corymbifera (fungus) / Gene: LCOR_04030.1 / Production host: Escherichia (bacteria) / Strain (production host): BL21 / References: UniProt: A0A068RQY7
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.06 Å3/Da / Density % sol: 59.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 40% v/v Polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97936 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 2024
RadiationMonochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97936 Å / Relative weight: 1
ReflectionResolution: 2.7→39.46 Å / Num. obs: 20318 / % possible obs: 100 % / Redundancy: 14.3 % / CC1/2: 0.993 / Rpim(I) all: 0.107 / Rrim(I) all: 0.414 / Χ2: 0.99 / Net I/σ(I): 7.6
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 15 % / Num. unique obs: 2635 / CC1/2: 0.616 / Rpim(I) all: 0.954 / Χ2: 0.94

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→39.46 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.897 / SU B: 20.048 / SU ML: 0.363 / Cross valid method: THROUGHOUT / ESU R: 0.633 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27989 1021 5 %RANDOM
Rwork0.22086 ---
obs0.2239 19244 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.409 Å2
Baniso -1Baniso -2Baniso -3
1-2.07 Å21.03 Å20 Å2
2--2.07 Å2-0 Å2
3----6.7 Å2
Refinement stepCycle: 1 / Resolution: 2.7→39.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3796 0 87 23 3906
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0123986
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163634
X-RAY DIFFRACTIONr_angle_refined_deg1.321.845421
X-RAY DIFFRACTIONr_angle_other_deg0.4731.7718315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2895482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.253541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.62210632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0580.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024803
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02947
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_it3.8046.1431937
X-RAY DIFFRACTIONr_mcbond_other3.8026.1431937
X-RAY DIFFRACTIONr_mcangle_it5.95511.0332416
X-RAY DIFFRACTIONr_mcangle_other5.95411.0332417
X-RAY DIFFRACTIONr_scbond_it4.1236.4732049
X-RAY DIFFRACTIONr_scbond_other4.1076.4832037
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.50611.7853006
X-RAY DIFFRACTIONr_long_range_B_refined8.58356.74278
X-RAY DIFFRACTIONr_long_range_B_other8.58456.734273
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 65 -
Rwork0.374 1389 -
obs--99.86 %

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