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- PDB-2cxk: Crystal structure of the TIG domain of human calmodulin-binding t... -

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Basic information

Entry
Database: PDB / ID: 2cxk
TitleCrystal structure of the TIG domain of human calmodulin-binding transcription activator 1 (CAMTA1)
Componentscalmodulin binding transcription activator 1
KeywordsTRANSCRIPTION / Structural genomics / TIG/IPT domain / transcription activator / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


positive regulation of calcineurin-NFAT signaling cascade / neuromuscular process controlling balance / transcription coregulator activity / double-stranded DNA binding / sequence-specific DNA binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
CG-1 DNA-binding domain / CG-1 domain / CG-1 DNA-binding domain profile. / CG-1 / IQ calmodulin-binding motif / IPT/TIG domain / IPT domain / IQ motif, EF-hand binding site / IQ motif profile. / Ankyrin repeats (3 copies) ...CG-1 DNA-binding domain / CG-1 domain / CG-1 DNA-binding domain profile. / CG-1 / IQ calmodulin-binding motif / IPT/TIG domain / IPT domain / IQ motif, EF-hand binding site / IQ motif profile. / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Calmodulin-binding transcription activator 1 / Calmodulin-binding transcription activator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsPioszak, A.A. / Murayama, K. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of the TIG domain of human calmodulin-binding transcription activator 1 (CAMTA1)
Authors: Pioszak, A.A. / Murayama, K. / Shirouzu, M. / Yokoyama, S.
History
DepositionJun 30, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 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 / struct_site
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 / _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

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Assembly

Deposited unit
A: calmodulin binding transcription activator 1
B: calmodulin binding transcription activator 1
C: calmodulin binding transcription activator 1
D: calmodulin binding transcription activator 1
E: calmodulin binding transcription activator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,29711
Polymers50,7205
Non-polymers5766
Water5,693316
1
A: calmodulin binding transcription activator 1
B: calmodulin binding transcription activator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4804
Polymers20,2882
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-22 kcal/mol
Surface area8310 Å2
MethodPISA
2
C: calmodulin binding transcription activator 1
D: calmodulin binding transcription activator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6726
Polymers20,2882
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-20 kcal/mol
Surface area8290 Å2
MethodPISA
3
E: calmodulin binding transcription activator 1

E: calmodulin binding transcription activator 1


Theoretical massNumber of molelcules
Total (without water)20,2882
Polymers20,2882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area1570 Å2
ΔGint-25 kcal/mol
Surface area8130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.882, 88.882, 107.538
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-1006-

SO4

21B-1005-

SO4

31B-1005-

SO4

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Components

#1: Protein
calmodulin binding transcription activator 1 / CAMTA1


Mass: 10144.050 Da / Num. of mol.: 5 / Fragment: TIG domain (residues 872-953)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAMTA1 / Plasmid: P030512-77 / Production host: Cell-free protein synthesis / References: UniProt: Q5VUE1, UniProt: Q9Y6Y1*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.28 Å3/Da / Density % sol: 41.211502 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: Ammonium sulfate, MES buffer, Cesium chloride, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.979092, 0.979445, 0.96400
DetectorType: RIGAKU JUPITER / Detector: CCD / Date: Dec 11, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9790921
20.9794451
30.9641
ReflectionResolution: 1.85→50 Å / Num. all: 36316 / Num. obs: 36316 / % possible obs: 96.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.069
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.323 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→46.01 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2416551.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1748 5 %RANDOM
Rwork0.226 ---
all0.239 34809 --
obs0.226 34809 92.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.5418 Å2 / ksol: 0.350724 e/Å3
Displacement parametersBiso mean: 22.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.59 Å20 Å20 Å2
2--1.59 Å20 Å2
3----3.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.85→46.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3286 0 30 316 3632
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.542
X-RAY DIFFRACTIONc_scbond_it2.122
X-RAY DIFFRACTIONc_scangle_it3.062.5
LS refinement shellResolution: 1.85→1.92 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.328 167 5.4 %
Rwork0.282 2918 -
obs--84.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3so4_fin.paramso4_fin.top

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