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- PDB-4f4j: Conversion of the enzyme guanylate kinase into a mitotic spindle ... -

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Basic information

Entry
Database: PDB / ID: 4f4j
TitleConversion of the enzyme guanylate kinase into a mitotic spindle orienting protein by a single mutation that inhibits gmp- induced closing
ComponentsGuanylate kinase
KeywordsTRANSFERASE / Phosphotransferase / GMP and ATP
Function / homology
Function and homology information


Azathioprine ADME / GDP biosynthetic process / guanylate kinase / Interconversion of nucleotide di- and triphosphates / purine nucleotide metabolic process / guanylate kinase activity / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Guanylate kinase / Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding domain / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. ...Guanylate kinase / Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding domain / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsJohnston, C.A. / Whitney, D. / Volkman, B.F. / Prehoda, K.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Conversion of the enzyme guanylate kinase into a mitotic-spindle orienting protein by a single mutation that inhibits GMP-induced closing.
Authors: Johnston, C.A. / Whitney, D.S. / Volkman, B.F. / Doe, C.Q. / Prehoda, K.E.
History
DepositionMay 10, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionJun 13, 2012ID: 3SQK
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Guanylate kinase
B: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3197
Polymers44,8382
Non-polymers4805
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-93 kcal/mol
Surface area20340 Å2
MethodPISA
2
A: Guanylate kinase
hetero molecules

B: Guanylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3197
Polymers44,8382
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z+1/41
Buried area3430 Å2
ΔGint-75 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.682, 103.682, 130.881
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Guanylate kinase / GMP kinase


Mass: 22419.205 Da / Num. of mol.: 2 / Fragment: GMP kinase (unp residues 1-187) / Mutation: S35P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: GUK1, YDR454C, D9461.39 / Production host: Escherichia coli (E. coli) / References: UniProt: P15454, guanylate kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.92 Å3/Da / Density % sol: 68.64 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.6M LiSO4, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 16, 2011
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 25356 / Num. obs: 24012 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.914 / SU B: 14.769 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.258 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25536 1344 5 %RANDOM
Rwork0.21597 ---
all0.219 25356 --
obs0.218 24012 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.682 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20 Å2
2--0.58 Å20 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2916 0 25 91 3032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222994
X-RAY DIFFRACTIONr_angle_refined_deg1.9061.9754039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1075372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.63224.884129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.87415527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8741512
X-RAY DIFFRACTIONr_chiral_restr0.130.2441
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212228
X-RAY DIFFRACTIONr_mcbond_it1.0261.51863
X-RAY DIFFRACTIONr_mcangle_it2.02423002
X-RAY DIFFRACTIONr_scbond_it3.41131131
X-RAY DIFFRACTIONr_scangle_it5.3754.51037
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 64 -
Rwork0.308 1847 -
obs--98.81 %
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)
11.04620.2205-0.03311.1715-0.52690.3336-0.0615-0.00140.0680.0155-0.024-0.00710.1315-0.0250.08550.11910.00940.04310.0199-0.02940.030433.9879-11.573143.0791
21.02810.16760.33210.518-0.26540.4187-0.05150.08520.16420.00630.10710.0969-0.0284-0.0614-0.05560.065-0.01710.02220.08620.03690.060235.392-5.785813.8818
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-3 - 185
2X-RAY DIFFRACTION1A201
3X-RAY DIFFRACTION1A301 - 347
4X-RAY DIFFRACTION2B-10 - 185

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