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- PDB-3en9: Structure of the Methanococcus jannaschii KAE1-BUD32 fusion protein -

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Basic information

Entry
Database: PDB / ID: 3en9
TitleStructure of the Methanococcus jannaschii KAE1-BUD32 fusion protein
ComponentsO-sialoglycoprotein endopeptidase/protein kinase
KeywordsHYDROLASE / endopeptidase activity / protein kinase activity / protein serine/threonine kinase activity / ATP binding / metallopeptidase activity / hydrolase activity / metal ion binding / Metal-binding / Metalloprotease / Protease / Zinc
Function / homology
Function and homology information


N6-L-threonylcarbamoyladenine synthase / N(6)-L-threonylcarbamoyladenine synthase activity / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / protein serine/threonine/tyrosine kinase activity / metalloendopeptidase activity / non-specific serine/threonine protein kinase / iron ion binding / phosphorylation / protein serine kinase activity ...N6-L-threonylcarbamoyladenine synthase / N(6)-L-threonylcarbamoyladenine synthase activity / EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / protein serine/threonine/tyrosine kinase activity / metalloendopeptidase activity / non-specific serine/threonine protein kinase / iron ion binding / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein / tRNA N6-adenosine threonylcarbamoyltransferase Kae1, archaea and eukaryote / Serine/threonine-protein kinase Bud32 / Peptidase M22, conserved site / Glycoprotease family signature. / Kae1/TsaD family / Gcp-like domain / tRNA N6-adenosine threonylcarbamoyltransferase / RIO1 family / ATPase, nucleotide binding domain ...Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein / tRNA N6-adenosine threonylcarbamoyltransferase Kae1, archaea and eukaryote / Serine/threonine-protein kinase Bud32 / Peptidase M22, conserved site / Glycoprotease family signature. / Kae1/TsaD family / Gcp-like domain / tRNA N6-adenosine threonylcarbamoyltransferase / RIO1 family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
HEXATANTALUM DODECABROMIDE / Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.67 Å
AuthorsNeculai, D.
CitationJournal: Mol.Cell / Year: 2008
Title: Atomic structure of the KEOPS complex: an ancient protein kinase-containing molecular machine.
Authors: Mao, D.Y. / Neculai, D. / Downey, M. / Orlicky, S. / Haffani, Y.Z. / Ceccarelli, D.F. / Ho, J.S. / Szilard, R.K. / Zhang, W. / Ho, C.S. / Wan, L. / Fares, C. / Rumpel, S. / Kurinov, I. / ...Authors: Mao, D.Y. / Neculai, D. / Downey, M. / Orlicky, S. / Haffani, Y.Z. / Ceccarelli, D.F. / Ho, J.S. / Szilard, R.K. / Zhang, W. / Ho, C.S. / Wan, L. / Fares, C. / Rumpel, S. / Kurinov, I. / Arrowsmith, C.H. / Durocher, D. / Sicheri, F.
History
DepositionSep 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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: O-sialoglycoprotein endopeptidase/protein kinase
B: O-sialoglycoprotein endopeptidase/protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,3956
Polymers122,2572
Non-polymers4,1384
Water1,63991
1
A: O-sialoglycoprotein endopeptidase/protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1973
Polymers61,1281
Non-polymers2,0692
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: O-sialoglycoprotein endopeptidase/protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1973
Polymers61,1281
Non-polymers2,0692
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.730, 148.730, 136.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-601-

TBR

21A-601-

TBR

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Components

#1: Protein O-sialoglycoprotein endopeptidase/protein kinase / Glycoprotease


Mass: 61128.418 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: DSM 2661 / Gene: gcp, MJ1130 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58530, EC: 3.4.24.57
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TBR / HEXATANTALUM DODECABROMIDE / DODECABROMOHEXATANTALUM


Mass: 2044.535 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br12Ta6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTBR 601 A IS LOCATED ON A CRYSTALLOGRAPHIC 2-FOLD AXIS, THEREFORE ONLY HALF OF IT WAS MODELED IN ...TBR 601 A IS LOCATED ON A CRYSTALLOGRAPHIC 2-FOLD AXIS, THEREFORE ONLY HALF OF IT WAS MODELED IN THE ASYMMETRIC UNIT.

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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: 3.09 Å3/Da / Density % sol: 60.13 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 10 mM HEPES 10% PEG3000, 11% spermine tetrahydrochloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97935
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 2, 2007 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.67→148.73 Å / Num. obs: 43971 / % possible obs: 99.8 % / Observed criterion σ(I): 3.23 / Redundancy: 1.88 % / Rmerge(I) obs: 0.0578 / Net I/σ(I): 20.06
Reflection shellResolution: 2.67→2.76 Å / Redundancy: 1.92 % / Rmerge(I) obs: 0.2286 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.2286 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXDphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XDSdata scaling
RefinementResolution: 2.67→65.294 Å / Occupancy max: 1 / Occupancy min: 0.25 / SU ML: 0.44 / Isotropic thermal model: Isotropic / σ(F): 18.8 / Phase error: 25.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2643 2213 5.03 %
Rwork0.202 --
obs0.2052 43966 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.23 Å2 / ksol: 0.336 e/Å3
Displacement parametersBiso mean: 72.125 Å2
Baniso -1Baniso -2Baniso -3
1--1.454 Å2-0 Å20 Å2
2---1.454 Å20 Å2
3---2.908 Å2
Refinement stepCycle: LAST / Resolution: 2.67→65.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8185 0 30 91 8306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0278432
X-RAY DIFFRACTIONf_angle_d1.25711492
X-RAY DIFFRACTIONf_dihedral_angle_d19.2033093
X-RAY DIFFRACTIONf_chiral_restr0.0871260
X-RAY DIFFRACTIONf_plane_restr0.0051442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-2.72810.34681420.28812576X-RAY DIFFRACTION100
2.7281-2.79160.36761330.26292552X-RAY DIFFRACTION100
2.7916-2.86140.31521350.24392559X-RAY DIFFRACTION100
2.8614-2.93870.31541260.23692581X-RAY DIFFRACTION100
2.9387-3.02520.281400.22322599X-RAY DIFFRACTION100
3.0252-3.12290.27351290.21532563X-RAY DIFFRACTION100
3.1229-3.23450.30791320.20222601X-RAY DIFFRACTION100
3.2345-3.3640.27711420.20982568X-RAY DIFFRACTION100
3.364-3.5170.24491430.20212597X-RAY DIFFRACTION100
3.517-3.70250.27661210.19082612X-RAY DIFFRACTION100
3.7025-3.93440.24031390.18092598X-RAY DIFFRACTION100
3.9344-4.23810.29171580.17912599X-RAY DIFFRACTION100
4.2381-4.66450.2531360.16782645X-RAY DIFFRACTION100
4.6645-5.33920.21951620.17072619X-RAY DIFFRACTION100
5.3392-6.72580.2511200.20412708X-RAY DIFFRACTION100
6.7258-65.31340.22961550.18932776X-RAY DIFFRACTION98
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)
10.4538-0.02110.09850.385-0.18261.98080.0098-0.0536-0.00140.0411-0.0901-0.12760.25490.25570.05630.2908-0.0433-0.00540.37650.04430.341229.194186.807965.9467
20.43160.8469-0.03441.99490.21280.0942-0.06550.06820.061-0.2899-0.03190.12580.02990.02670.07840.47950.002-0.01760.3857-0.00730.391939.14142.656259.3846
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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