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- PDB-2xz2: Crystal structure of CstF-50 homodimerization domain -

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Basic information

Entry
Database: PDB / ID: 2xz2
TitleCrystal structure of CstF-50 homodimerization domain
ComponentsCSTF-50, ISOFORM B
KeywordsRNA BINDING PROTEIN / RNA-BINDING PROTEIN / 3' END MRNA MATURATION / TRANSCRIPTION
Function / homologyCleavage stimulation factor subunit 1, dimerisation domain / Mitochondrial Import Receptor Subunit Tom20; Chain A / Up-down Bundle / Mainly Alpha / DI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsMoreno-Morcillo, M. / Fribourg, S.
CitationJournal: RNA / Year: 2011
Title: Hexameric Architecture of Cstf Supported by Cstf- 50 Homodimerization Domain Structure.
Authors: Moreno-Morcillo, M. / Minvielle-Sebastia, L. / Mackereth, C. / Fribourg, S.
History
DepositionNov 22, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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 / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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: CSTF-50, ISOFORM B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8466
Polymers7,6481
Non-polymers1985
Water72140
1
A: CSTF-50, ISOFORM B
hetero molecules

A: CSTF-50, ISOFORM B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,69212
Polymers15,2962
Non-polymers39610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area4290 Å2
ΔGint-128 kcal/mol
Surface area8230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.230, 52.230, 57.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein CSTF-50, ISOFORM B


Mass: 7648.064 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-65
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8IMG2
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.54 Å3/Da / Density % sol: 0.51 % / Description: NONE
Crystal growpH: 7.5
Details: 100 MM HEPES PH 7.5, 3% PEG400, 1.4 M AMMONIUM SULFATE, 15% GLYCEROL

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9184
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 13968 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 3.52 % / Biso Wilson estimate: 13.97 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 21.56
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 5.19 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 5.13 / % possible all: 99.3

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
XDSdata reduction
SCALEPACKdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.4→12.13 Å / Cor.coef. Fo:Fc: 0.9489 / Cor.coef. Fo:Fc free: 0.893 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2452 702 5.03 %RANDOM
Rwork0.1989 ---
obs0.2012 7738 --
Displacement parametersBiso mean: 19.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.5921 Å20 Å20 Å2
2--1.2175 Å20 Å2
3----0.6254 Å2
Refine analyzeLuzzati coordinate error obs: 0.168 Å
Refinement stepCycle: LAST / Resolution: 1.4→12.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms525 0 11 40 576
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01568HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.99762HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d217SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes14HARMONIC2
X-RAY DIFFRACTIONt_gen_planes81HARMONIC5
X-RAY DIFFRACTIONt_it568HARMONIC20
X-RAY DIFFRACTIONt_nbd5SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.01
X-RAY DIFFRACTIONt_other_torsion17.14
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion72SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact718SEMIHARMONIC4
LS refinement shellResolution: 1.4→1.51 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2282 146 5.21 %
Rwork0.2142 2658 -
all0.2149 2804 -

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