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- PDB-2j7j: Invariance of the zinc finger module: a comparison of the free st... -

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Basic information

Entry
Database: PDB / ID: 2j7j
TitleInvariance of the zinc finger module: a comparison of the free structure with those in nucleic-acid complexes
ComponentsTRANSCRIPTION FACTOR IIIA
KeywordsTRANSCRIPTION / ZINC FINGER MODULE / ALTERNATIVE INITIATION / NUCLEAR PROTEIN / PHOSPHORYLATION / HYDROPHOBIC CORE / ZINC / RNA-BINDING / ZINC-FINGER / DNA-BINDING / TRANSCRIPTION REGULATION / POLYMORPHISM / METAL-BINDING
Function / homology
Function and homology information


ribosomal large subunit biogenesis / DNA binding / RNA binding / zinc ion binding / nucleus
Similarity search - Function
: / TFIIIA, beta-beta-alpha zinc finger / : / Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. ...: / TFIIIA, beta-beta-alpha zinc finger / : / Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcription factor IIIA
Similarity search - Component
Biological speciesXENOPUS LAEVIS (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsLu, D. / Klug, A.
CitationJournal: Proteins / Year: 2007
Title: Invariance of the Zinc Finger Module: A Comparison of the Free Structure with Those in Nucleic-Acid Complexes.
Authors: Lu, D. / Klug, A.
History
DepositionOct 10, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_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: TRANSCRIPTION FACTOR IIIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3495
Polymers10,0571
Non-polymers2924
Water2,306128
1
A: TRANSCRIPTION FACTOR IIIA
hetero molecules

A: TRANSCRIPTION FACTOR IIIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,69810
Polymers20,1132
Non-polymers5858
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_675x-y+1,-y+2,-z1
Buried area2840 Å2
ΔGint-37.5 kcal/mol
Surface area11380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.954, 50.954, 173.431
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein TRANSCRIPTION FACTOR IIIA / FACTOR A / TFIIIA / S-TFIIIA/O-TFIIIA


Mass: 10056.620 Da / Num. of mol.: 1 / Fragment: ZINC FINGER 4-6, RESIDUES 127-210
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) XENOPUS LAEVIS (African clawed frog) / Cell: OOCYTE / Plasmid: PET13A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03001
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 3.23 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 8.5 / Details: 1.6M (NH4)2SO4, 25MM MGSO4, 50MM TRIS.HCL PH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9791, 1.2824, 1.2828, 1.2651
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 24, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
21.28241
31.28281
41.26511
ReflectionResolution: 1.65→57.83 Å / Num. obs: 17038 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 9.5 % / Biso Wilson estimate: 18.03 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.2
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 10 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.65→44.28 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.828 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.094 / ESU R Free: 0.088
Stereochemistry target values: MAXIMUM LIKELIHOODWITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 858 5.1 %RANDOM
Rwork0.217 ---
obs0.218 16099 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.99 Å2
Baniso -1Baniso -2Baniso -3
1-1.42 Å20.71 Å20 Å2
2--1.42 Å20 Å2
3----2.12 Å2
Refinement stepCycle: LAST / Resolution: 1.65→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms703 0 8 128 839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.021742
X-RAY DIFFRACTIONr_bond_other_d0.0020.02610
X-RAY DIFFRACTIONr_angle_refined_deg0.8781.917996
X-RAY DIFFRACTIONr_angle_other_deg0.69431448
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.517584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0550.296
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02806
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02156
X-RAY DIFFRACTIONr_nbd_refined0.1830.2152
X-RAY DIFFRACTIONr_nbd_other0.2070.2634
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0790.2394
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.285
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2980.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1130.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.621.5425
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1962687
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3623317
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2664.5309
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.251 71
Rwork0.252 1143

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