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- PDB-3eno: Crystal structure of Pyrococcus furiosus Pcc1 in complex with The... -

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Basic information

Entry
Database: PDB / ID: 3eno
TitleCrystal structure of Pyrococcus furiosus Pcc1 in complex with Thermoplasma acidophilum Kae1
Components
  • Putative O-sialoglycoprotein endopeptidase
  • uncharacterized protein PF2011
Keywordshydrolase/unknown function / Hydrolase / Metal-binding / Metalloprotease / Protease / Zinc / KEOPS complex / ATPase / metal ion binding / dimerization module / telomere / hydrolase-unknown function COMPLEX
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 / protein serine/threonine kinase activity / zinc ion binding ...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 / protein serine/threonine kinase activity / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function
tRNA N6-adenosine threonylcarbamoyltransferase Kae1, archaea / Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein / tRNA N6-adenosine threonylcarbamoyltransferase Kae1, archaea and eukaryote / Serine/threonine-protein kinase Bud32 / CTAG/Pcc1 family / Transcription factor Pcc1 / Kae1/TsaD family / Gcp-like domain / tRNA N6-adenosine threonylcarbamoyltransferase / Alpha-D-phosphohexomutase, C-terminal domain ...tRNA N6-adenosine threonylcarbamoyltransferase Kae1, archaea / Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein / tRNA N6-adenosine threonylcarbamoyltransferase Kae1, archaea and eukaryote / Serine/threonine-protein kinase Bud32 / CTAG/Pcc1 family / Transcription factor Pcc1 / Kae1/TsaD family / Gcp-like domain / tRNA N6-adenosine threonylcarbamoyltransferase / Alpha-D-phosphohexomutase, C-terminal domain / TATA-Binding Protein / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
KEOPS complex subunit Pcc1 / Probable bifunctional tRNA threonylcarbamoyladenosine biosynthesis protein
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
Pyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.0201 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 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative O-sialoglycoprotein endopeptidase
B: Putative O-sialoglycoprotein endopeptidase
C: uncharacterized protein PF2011
D: uncharacterized protein PF2011
E: uncharacterized protein PF2011
F: uncharacterized protein PF2011
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,7648
Polymers111,7166
Non-polymers492
Water00
1
A: Putative O-sialoglycoprotein endopeptidase
C: uncharacterized protein PF2011
D: uncharacterized protein PF2011
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8824
Polymers55,8583
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-24 kcal/mol
Surface area21330 Å2
MethodPISA
2
B: Putative O-sialoglycoprotein endopeptidase
E: uncharacterized protein PF2011
F: uncharacterized protein PF2011
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8824
Polymers55,8583
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-24 kcal/mol
Surface area21110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.560, 66.560, 435.559
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Putative O-sialoglycoprotein endopeptidase / E.C.3.4.24.57 / Kae1 / Glycoprotease


Mass: 36056.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Strain: DSM 1728 / Gene: gcp, TA0324 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HLA5, EC: 3.4.24.57
#2: Protein
uncharacterized protein PF2011 / Pcc1


Mass: 9900.515 Da / Num. of mol.: 4 / Mutation: I12M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Gene: PF2011 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8TZI1
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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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: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M NaCl, 40% PEG300, 0.1M HEPES, 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-E / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2008 / Details: mirrors
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
Reflection twinType: pseudo-merohedral / Operator: h,-h-k,-l / Fraction: 0.435
ReflectionResolution: 3.0201→435.1 Å / Num. all: 21248 / Num. obs: 21243 / % possible obs: 100 % / Observed criterion σ(I): 2.18 / Redundancy: 1.97 % / Rmerge(I) obs: 0.0461 / Rsym value: 0.0461 / Net I/σ(I): 14.91
Reflection shellResolution: 3.0201→3.12 Å / Redundancy: 1.94 % / Rmerge(I) obs: 0.2948 / Mean I/σ(I) obs: 2.41 / Num. unique all: 1936 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IVP, pFu pcc1 dimeric structure

2ivp


Resolution: 3.0201→39.581 Å / Cross valid method: THROUGHOUT / σ(F): 0.2 / Phase error: 37.69 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2818 2142 5.31 %RANDOM
Rwork0.243 ---
all0.24501 ---
obs0.245 21243 95.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.862 Å2 / ksol: 0.325 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.9047 Å20 Å20 Å2
2--10.9047 Å20 Å2
3----29.0246 Å2
Refinement stepCycle: LAST / Resolution: 3.0201→39.581 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7469 0 2 0 7471
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047585
X-RAY DIFFRACTIONf_angle_d0.8410248
X-RAY DIFFRACTIONf_chiral_restr0.0561200
X-RAY DIFFRACTIONf_plane_restr0.0041299
X-RAY DIFFRACTIONf_dihedral_angle_d18.6592822
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0201-3.07220.40721130.35481769X-RAY DIFFRACTION98
3.0722-3.1280.4159830.33821938X-RAY DIFFRACTION98
3.128-3.18820.3046790.3261922X-RAY DIFFRACTION98
3.1882-3.25320.30281090.30551842X-RAY DIFFRACTION98
3.2532-3.32390.30671060.29471973X-RAY DIFFRACTION98
3.3239-3.40120.33821080.29651804X-RAY DIFFRACTION98
3.4012-3.48620.30351200.28071931X-RAY DIFFRACTION98
3.4862-3.58040.2412900.27391893X-RAY DIFFRACTION98
3.5804-3.68570.2801990.26941943X-RAY DIFFRACTION98
3.6857-3.80460.3371920.26821867X-RAY DIFFRACTION98
3.8046-3.94040.2705900.24161943X-RAY DIFFRACTION98
3.9404-4.0980.33131060.23131913X-RAY DIFFRACTION98
4.098-4.28430.29391110.2481915X-RAY DIFFRACTION98
4.2843-4.50990.29811150.21981914X-RAY DIFFRACTION98
4.5099-4.7920.22081060.20941929X-RAY DIFFRACTION98
4.792-5.16130.2484820.21781920X-RAY DIFFRACTION98
5.1613-5.67930.3587910.25291941X-RAY DIFFRACTION98
5.6793-6.4980.27491060.26851969X-RAY DIFFRACTION98
6.498-8.1750.3057870.21342006X-RAY DIFFRACTION98
8.175-39.58390.20881370.18321968X-RAY DIFFRACTION98

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