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- PDB-9d8a: Structure of Rhizopus azygosporus Kinase in complex with GDP and MG -

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Basic information

Entry
Database: PDB / ID: 9d8a
TitleStructure of Rhizopus azygosporus Kinase in complex with GDP and MG
ComponentsRhizopus azygosporus Kinase
KeywordsTRANSFERASE / kinase / GTP specific / tRNA splicing
Function / homologyAAA domain / P-loop containing nucleoside triphosphate hydrolase / GUANOSINE-5'-DIPHOSPHATE / Uncharacterized protein
Function and homology information
Biological speciesRhizopus azygosporus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsWimberly-Gard, G.M. / Shuman, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM126945 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM134021 United States
CitationJournal: To Be Published
Title: Structure of Rhizopus azygosporus Kinase in complex with GDP and MG
Authors: Wimberly-Gard, G.M. / Shuman, S.
History
DepositionAug 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rhizopus azygosporus Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7623
Polymers20,2941
Non-polymers4682
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.417, 66.460, 73.703
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Rhizopus azygosporus Kinase


Mass: 20294.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizopus azygosporus (fungus) / Gene: CU097_007847 / Plasmid: pET SUMO / Details (production host): HIS10 SMT3 tag / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A367K070
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M NH4Cl, 20% (w/v) PEG-3350, PEG 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: 0.9793 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Aug 6, 2024 / Details: M
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.65→34.76 Å / Num. obs: 26297 / % possible obs: 100 % / Redundancy: 12.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.044 / Rrim(I) all: 0.157 / Χ2: 1.03 / Net I/av σ(I): 10 / Net I/σ(I): 10
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 12.3 % / Rmerge(I) obs: 4.708 / Num. unique obs: 1199 / CC1/2: 0.375 / Rpim(I) all: 1.388 / Χ2: 1.07 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimless0.7.15data scaling
XDS6.2017data reduction
PHASER2.8.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.941 / SU B: 6.331 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23727 1181 4.9 %RANDOM
Rwork0.16941 ---
obs0.17256 22793 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.587 Å2
Baniso -1Baniso -2Baniso -3
1--2.54 Å20 Å2-0 Å2
2---0.23 Å20 Å2
3---2.77 Å2
Refinement stepCycle: 1 / Resolution: 1.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1355 0 29 94 1478
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121415
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161343
X-RAY DIFFRACTIONr_angle_refined_deg1.6481.8731910
X-RAY DIFFRACTIONr_angle_other_deg0.5931.7963101
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5485171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.34511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.34210258
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021626
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02302
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_it8.7283.219687
X-RAY DIFFRACTIONr_mcbond_other8.6133.218687
X-RAY DIFFRACTIONr_mcangle_it12.285.793857
X-RAY DIFFRACTIONr_mcangle_other12.2785.796858
X-RAY DIFFRACTIONr_scbond_it10.053.564728
X-RAY DIFFRACTIONr_scbond_other10.0423.57724
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.5396.3781054
X-RAY DIFFRACTIONr_long_range_B_refined20.95534.321569
X-RAY DIFFRACTIONr_long_range_B_other19.98133.591544
X-RAY DIFFRACTIONr_rigid_bond_restr4.01932758
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 79 -
Rwork0.302 1633 -
obs--99.94 %

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