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- PDB-1rqf: Structure of CK2 beta subunit crystallized in the presence of a p... -

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Basic information

Entry
Database: PDB / ID: 1rqf
TitleStructure of CK2 beta subunit crystallized in the presence of a p21WAF1 peptide
Components
  • (Disordered segment of Cyclin-dependent kinase inhibitor ...) x 3
  • Casein kinase II beta chain
KeywordsTRANSFERASE / CASEIN KINASE BETA SUBUNIT / SER/THR PROTEIN KINASE / CYCLIN-DEPENDENT KINASE INHIBITOR / ZN FINGER
Function / homology
Function and homology information


protein kinase regulator activity / protein kinase CK2 complex / Wnt signaling pathway / metal ion binding
Similarity search - Function
protein kinase ck2 holoenzyme, chain C, domain 1 / protein kinase ck2 holoenzyme, chain C, domain 1 / Casein kinase II, regulatory subunit / Casein kinase II, regulatory subunit, N-terminal / Casein kinase II subunit beta-like / Casein kinase II regulatory subunit / Casein kinase II regulatory subunit signature. / Casein kinase II regulatory subunit / N-terminal domain of TfIIb - #20 / N-terminal domain of TfIIb ...protein kinase ck2 holoenzyme, chain C, domain 1 / protein kinase ck2 holoenzyme, chain C, domain 1 / Casein kinase II, regulatory subunit / Casein kinase II, regulatory subunit, N-terminal / Casein kinase II subunit beta-like / Casein kinase II regulatory subunit / Casein kinase II regulatory subunit signature. / Casein kinase II regulatory subunit / N-terminal domain of TfIIb - #20 / N-terminal domain of TfIIb / Single Sheet / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
UNKNOWN / Casein kinase II subunit beta
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsBertrand, L. / Sayed, M.F. / Pei, X.-Y. / Parisini, E. / Dhanaraj, V. / Bolanos-Garcia, V.M. / Allende, J.E. / Blundell, T.L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of the regulatory subunit of CK2 in the presence of a p21WAF1 peptide demonstrates flexibility of the acidic loop.
Authors: Bertrand, L. / Sayed, M.F. / Pei, X.Y. / Parisini, E. / Dhanaraj, V. / Bolanos-Garcia, V.M. / Allende, J.E. / Blundell, T.L.
History
DepositionDec 5, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The complete sequence crystallized by the authors for chains M,N,O,P,Q,R,S,T is ...SEQUENCE The complete sequence crystallized by the authors for chains M,N,O,P,Q,R,S,T is RERWNFDFVTETPLEGDFAW (residues 46-65 of reference sequence SwissProt P38936). The authors informed that they do not know how the coordinates align with the sequence since they could not identify the side chains of the residues they could see, and since the rest of the residues are disordered. Each group of unknown residues has been assigned a unique chain ID and is believed to be part of one chain. UNK Q 1 and UNK R 1 are the only visible residues in chains Q and R, respectively.
Remark 300 BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ... BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 16 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Casein kinase II beta chain
B: Casein kinase II beta chain
D: Casein kinase II beta chain
E: Casein kinase II beta chain
G: Casein kinase II beta chain
H: Casein kinase II beta chain
J: Casein kinase II beta chain
K: Casein kinase II beta chain
M: Disordered segment of Cyclin-dependent kinase inhibitor 1
N: Disordered segment of Cyclin-dependent kinase inhibitor 1
O: Disordered segment of Cyclin-dependent kinase inhibitor 1
P: Disordered segment of Cyclin-dependent kinase inhibitor 1
S: Disordered segment of Cyclin-dependent kinase inhibitor 1
T: Disordered segment of Cyclin-dependent kinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,13024
Polymers172,40114
Non-polymers73010
Water1,17165
1
A: Casein kinase II beta chain
B: Casein kinase II beta chain
M: Disordered segment of Cyclin-dependent kinase inhibitor 1
N: Disordered segment of Cyclin-dependent kinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3686
Polymers43,2374
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Casein kinase II beta chain
E: Casein kinase II beta chain
O: Disordered segment of Cyclin-dependent kinase inhibitor 1
P: Disordered segment of Cyclin-dependent kinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7267
Polymers43,4924
Non-polymers2343
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Casein kinase II beta chain
H: Casein kinase II beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7545
Polymers42,5202
Non-polymers2343
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Casein kinase II beta chain
K: Casein kinase II beta chain
S: Disordered segment of Cyclin-dependent kinase inhibitor 1
T: Disordered segment of Cyclin-dependent kinase inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2836
Polymers43,1524
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.422, 170.626, 74.546
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe asymmetric unit contains 4 biological dimers of CK2 regulatory subunit

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Components

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Protein , 1 types, 8 molecules ABDEGHJK

#1: Protein
Casein kinase II beta chain / CK II / Phosvitin


Mass: 21259.990 Da / Num. of mol.: 8 / Fragment: REGULATORY SUBUNIT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: KC2B / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P28021, EC: 2.7.1.37

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Disordered segment of Cyclin-dependent kinase inhibitor ... , 3 types, 6 molecules MNTOPS

#2: Protein/peptide Disordered segment of Cyclin-dependent kinase inhibitor 1 / p21WAF1


Mass: 358.434 Da / Num. of mol.: 3 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide occurs naturally in Homo sapiens (human).
#3: Protein/peptide Disordered segment of Cyclin-dependent kinase inhibitor 1 / p21WAF1


Mass: 698.854 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide occurs naturally in Homo sapiens (human).
#4: Protein/peptide Disordered segment of Cyclin-dependent kinase inhibitor 1 / p21WAF1


Mass: 273.330 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide occurs naturally in Homo sapiens (human).

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Non-polymers , 3 types, 75 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-UNK / UNKNOWN


Type: L-peptide linking / Mass: 103.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.68 Å3/Da / Density % sol: 54.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.2
Details: PEG 4000, bicine, magnesium chloride, DTT, isopropanol, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 5, 2001 / Details: multilayer
RadiationMonochromator: GERMANIUM 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.89→11.97 Å / Num. all: 41529 / Num. obs: 41256 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 4.2 % / Biso Wilson estimate: 88.3 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 7.2
Reflection shellResolution: 2.89→3.08 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 2.2 / Num. unique all: 6741 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ProDCdata collection
SCALAdata scaling
MOLREPphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QF8

1qf8


Resolution: 2.89→11.97 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Used maximum likelihood with amplitudes procedure.
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2048 -shells
Rwork0.238 ---
obs0.24 41256 100 %-
all-41256 --
Displacement parametersBiso mean: 80.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 2.89→11.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11131 0 20 65 11216
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2.89→3.08 Å / Rfactor Rfree error: 0.021
RfactorNum. reflection% reflection
Rfree0.371 2048 -
Rwork0.362 --
obs-6741 99.8 %

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