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PDB | 3KGT | V30M mutant human transthyretin (TTR) complexed with genistein (V30M:GEN) pH 7.5

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Internal ID
69040
PDB Entry ID
3KGT
Title
V30M mutant human transthyretin (TTR) complexed with genistein (V30M:GEN) pH 7.5
Authors
Trivella, D.B.,Polikarpov, I.
Primary Citation
AuthorsTrivella, D.B., Bleicher, L., Palmieri, L.C., Wiggers, H.J., Montanari, C.A., Kelly, J.W., Lima, L.M., Foguel, D., Polikarpov, I.
TitleConformational differences between the wild type and V30M mutant transthyretin modulate its binding to genistein: implications to tetramer stability and ligand-binding.
JournalJ.Struct.Biol., v.170, pp.522 - 531, 2010
AbstractView
Pubmed20211733
DOI10.1016/j.jsb.2010.03.002
 
History
Deposition: 2009-10-29Release: 2010-03-23Last Modified: 2010-05-19
Experimental Method
TypeX-RAY DIFFRACTION
Parameters
Resolution [Å]R-Value (Obs.)R-Value (Work)R-FreeSpace Group
1.950.1990.1960.241P 21 21 2
Unit Cell
Length [Å]a43.27b85.07c64.18
Angles [°]alpha90.00beta90.00gamma90.00
Molecular Description
PolymerMoleculeMutationFragmentChainsEC NumberOther details
1TransthyretinV30MUNP residues 21-147A, B
Functional Class
Source
PolymerScientific NameCommon NameExpression System
1Homo sapienshumanEscherichia coli
Related PDB Entries
Chemical Component
IdentifierNameFormulaLigand StructureLigand Interaction
GENGENISTEINC15H10O5[View][View]
SCOP Classification
CATH Classification
Structural Details
KeywordTRANSPORT PROTEIN
TextTRANSPORT PROTEIN, TTR, TRANSTHYRETIN, AMYLOID, Amyloidosis, Disease mutation, Hormone, Neuropathy, Secreted, Thyroid hormone, Transport
 
Polymeric Molecules
Chain A
DescriptionTransthyretin
FragmentUNP residues 21-147
MutationV30M
Polymer typepolypeptide
Formula Weight13809.6
Source Methodgenetically manipulated
Entity NamePrealbumin, TBPA, TTR, ATTR
Entity Name Sysn/a
 
Chain B
DescriptionTransthyretin
FragmentUNP residues 21-147
MutationV30M
Polymer typepolypeptide
Formula Weight13809.6
Source Methodgenetically manipulated
Entity NamePrealbumin, TBPA, TTR, ATTR
Entity Name Sysn/a
 
Entity Poly
EntityChiralityLinkageMonomer# Mon.StrandTypeDetails
1n/anonon/aA,Bpolypeptide(L)n/a
Ligands And Prosthetic Groups
IDNameFormulaWeightLigand Structure
GENGENISTEINC15H10O5270.241View
Natural/Genetically Modified Source
Common Namehuman
Scientific NameHomo sapiens
Source Genusn/a
GenePALB, TTR
Host Common Namen/a
Host Scientific NameEscherichia coli
Host Genusn/a
Host Cell Linen/a
Host StrainBL21(DE3)
Host Vector Typeplasmid
Host Plasmidn/a
 
Crystallization Experiments
Methodvapor diffusion, hanging drop
PH7.5
Temperature293.0
Details0.2 M CaCl2, 0.1 M HEPES pH 7.5, 28% PEG 400, vapor diffusion, hanging drop, temperature 293K
 
Unit Cell
Length a (Å)Length b Å)Length c (Å)
43.2785.0764.18
Angle Alpha (°)Angle Beta (°)Angle Gamma (°)
90.0090.0090.00
Space Group
P 21 21 2
Diffraction Detector
DetectorCCD
TypeMAR CCD 165 mm
Detailsn/a
Collection Date2009-03-15
 
Diffraction Radiation
Monochromatorn/a
Diffraction ProtocolSINGLE WAVELENGTH
Wavelengthn/a
Wavelength List1.4586
 
Diffraction Source
SourceSYNCHROTRON
TypeLNLS BEAMLINE D03B-MX1
SiteLNLS
BeamlineD03B-MX1
 
Reflection Details
Observed Criterion Sigma (F)n/a
Observed Criterion Sigma (I)n/a
Resolution (High)1.95
Resolution (Low)30.00
Number Reflections (All) n/a
Number Reflections (Observed)17463
Percent Possible (Observed)97.7
R Merge I (Observed)0.073
Net I Over Average Sigma (I)n/a
B (Isotropic) From Wilson Plotn/a
Redundancy4.3
 
High Resolution Shell Details
Resolution(High)1.95
Resolution(Low)2.02
Percent Possible(All) n/a
R Merge I(Observed)0.073
Mean I Over Sigma(Observed)n/a
R Sym I(Observed)n/a
Redundancy4.3
Num Unique Reflections(All)n/a
 
Refinement Statistics
Structure Solution Methodn/a
Resolution (High)1.95
Resolution (Low)28.36
Cut-off Sigma (F)n/a
Cut-off Sigma (I)n/a
Number of Reflections (All)n/a
Number of Reflections (Observed)17392
Number of Reflections (R-Free) 884
Percent Reflections (Observed)97.00
R-Factor (All)n/a
R-Factor (Observed)0.199
R-Work0.196
R-Free0.241
R-Free Selection Detailsn/a
 
Temperature Factor Modeling
Isotropic Thermal Modeln/a
Mean Isotropic B Value24.310
Anisotropic B[1][1]0.00
Anisotropic B[1][2]0.00
Anisotropic B[1][3]0.00
Anisotropic B[2][2]0.01
Anisotropic B[2][3]0.00
Anisotropic B[3][3]-0.01
 
Resolution Shells
Shell Resol (High)1.95
Shell Resolution (Low)n/a
Number of Reflections (Observed)n/a
Number of Reflections (R-Free)63
Number of Reflections (R-Work)1170
R-Factor (R-Work)0.238
R-Factor (R-Free)0.326
R-Free Errorn/a
Percent Reflections (Observed)96.63
 
RMS Deviations
First|Previous|1 of 4|Next|Last|
Parameter TypeDeviation From Ideal
r_bond_refined_d0.009
r_bond_other_dn/a
r_angle_refined_deg1.163
r_angle_other_degn/a
r_dihedral_angle_1_deg5.584
r_dihedral_angle_2_deg31.417
r_dihedral_angle_3_deg14.494
r_dihedral_angle_4_deg10.361
r_chiral_restr0.076
r_gen_planes_refined0.005
First|Previous|1 of 4|Next|Last|
Number of Non-Hydrogen Atoms Used in Refinement
Protein Atoms1769
Nucleic Acid Atoms0
Heterogen Atoms40
Solvent Atoms155
 
Programs
Data Collectionn/a
Data Reduction (intensity integration)n/a
Data Reduction (data scaling)n/a
Structure Solutionn/a
Structure RefinementREFMAC 5.5.0102
 
Software
Classificationrefinement
Software NameREFMAC5
Software Version 5.2.0019
 
Classificationdata extraction
Software Namepdb_extract
Software Version 3.005
 
Sequence Chain
A
Sequence
  1   GPTGTGESKC  PLMVKVLDAV  RGSPAINVAM  HVFRKAADDT  WEPFASGKTS  ESGELHGLTT

 61   EEEFVEGIYK  VEIDTKSYWK  ALGISPFHEH  AEVVFTANDS  GPRRYTIAAL  LSPYSYSTTA

121   VVTNPKE  

Sequence Chain
B
Sequence
  1   GPTGTGESKC  PLMVKVLDAV  RGSPAINVAM  HVFRKAADDT  WEPFASGKTS  ESGELHGLTT

 61   EEEFVEGIYK  VEIDTKSYWK  ALGISPFHEH  AEVVFTANDS  GPRRYTIAAL  LSPYSYSTTA

121   VVTNPKE