[English] 日本語
Yorodumi
- PDB-3enp: Crystal structure of human cgi121 -

+
Open data


ID or keywords:

Loading...

-
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 / cytosol / cytoplasm
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / Water


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more