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- PDB-3enp: Crystal structure of human cgi121 -

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Basic information

Entry
Database: PDB / ID: 3enp
TitleCrystal structure of human cgi121
ComponentsTP53RK-binding protein
KeywordsHYDROLASE / KEOPS complex telomere kinase regulator / Nucleus
Function / homology
Function and homology information


EKC/KEOPS complex / tRNA threonylcarbamoyladenosine modification / tRNA modification in the nucleus and cytosol / protein kinase binding / nucleus / cytoplasm / cytosol
Similarity search - Function
PF0523-like / CGI121/TPRKB / CGI121/TPRKB / CGI121/TPRKB superfamily / Kinase binding protein CGI-121 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
EKC/KEOPS complex subunit TPRKB
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.48 Å
AuthorsHaffani, Y.Z. / Ceccarelli, D.F. / Neculai, D. / Mao, D.Y. / Sicheri, F.
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: Advisory / Version format compliance
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TP53RK-binding protein
B: TP53RK-binding protein


Theoretical massNumber of molelcules
Total (without water)40,0932
Polymers40,0932
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-18 kcal/mol
Surface area16480 Å2
MethodPISA
2
A: TP53RK-binding protein


Theoretical massNumber of molelcules
Total (without water)20,0471
Polymers20,0471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: TP53RK-binding protein


Theoretical massNumber of molelcules
Total (without water)20,0471
Polymers20,0471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.521, 93.521, 87.155
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein TP53RK-binding protein / PRPK-binding protein


Mass: 20046.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CGI-121, My019, TPRKB / Plasmid: pGEX-4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: Q9Y3C4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.76 Å3/Da / Density % sol: 55.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG 1500, 0.2 M CaOAc, 0.1 M imidazole, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 10, 2004 / Details: mirrors
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.48→31.88 Å / Num. all: 13866 / Num. obs: 13866 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.62 % / Rmerge(I) obs: 0.0494 / Net I/σ(I): 15.01
Reflection shellResolution: 2.48→2.58 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.53 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXDphasing
REFMAC5.4.0066refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.48→30.61 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.929 / SU B: 25.581 / SU ML: 0.258 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.434 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25741 779 5.1 %RANDOM
Rwork0.21096 ---
obs0.21336 14618 99.84 %-
all-13866 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.801 Å2
Baniso -1Baniso -2Baniso -3
1-1.71 Å20.85 Å20 Å2
2--1.71 Å20 Å2
3----2.56 Å2
Refinement stepCycle: LAST / Resolution: 2.48→30.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2636 0 0 18 2654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222667
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.9933557
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9655323
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.23226.214103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.69615501
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.56158
X-RAY DIFFRACTIONr_chiral_restr0.1190.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211824
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.6251.51712
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.08422722
X-RAY DIFFRACTIONr_scbond_it1.8823955
X-RAY DIFFRACTIONr_scangle_it2.9894.5835
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.48→2.544 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 70 -
Rwork0.354 1039 -
obs--99.37 %
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)
12.9675-0.78662.28295.19530.86215.73540.23350.3942-0.3573-0.6942-0.21640.67020.2435-0.2917-0.01720.01380.002-0.1006-0.092-0.03140.141518.59724.81639.727
23.42580.02921.85022.31170.3374.69020.0883-0.3255-0.28290.34220.00040.21770.6269-0.0022-0.0887-0.02320.01160.0948-0.12350.0797-0.101336.27222.12169.507
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 175
2X-RAY DIFFRACTION2B1 - 175

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