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- PDB-2apt: Crystal Structure of the G17E/S54N/K66E/Q72H/E80V/L81S/T87S/G96V ... -

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Basic information

Entry
Database: PDB / ID: 2apt
TitleCrystal Structure of the G17E/S54N/K66E/Q72H/E80V/L81S/T87S/G96V variant of the murine T cell receptor V beta 8.2 domain
ComponentsT-cell receptor beta chain V
KeywordsIMMUNE SYSTEM / the murine T cell receptor V beta 8.2 domain
Function / homology
Function and homology information


adaptive immune response
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
MALONIC ACID / Variable region-beta 8.5
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCho, S. / Swaminathan, C.P. / Yang, J. / Kerzic, M.C. / Guan, R. / Kieke, M.C. / Kranz, D.M. / Mariuzza, R.A. / Sundberg, E.J.
CitationJournal: Structure / Year: 2005
Title: Structural basis of affinity maturation and intramolecular cooperativity in a protein-protein interaction.
Authors: Cho, S. / Swaminathan, C.P. / Yang, J. / Kerzic, M.C. / Guan, R. / Kieke, M.C. / Kranz, D.M. / Mariuzza, R.A. / Sundberg, E.J.
History
DepositionAug 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 29, 2015Group: Non-polymer description
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Remark 999SEQUENCE NO SUITABLE SEQUENCE DATABASE REFERENCE WAS AVAILABLE AT THE TIME OF PROCESSING THIS FILE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T-cell receptor beta chain V
B: T-cell receptor beta chain V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4173
Polymers24,3132
Non-polymers1041
Water1,71195
1
A: T-cell receptor beta chain V


Theoretical massNumber of molelcules
Total (without water)12,1561
Polymers12,1561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: T-cell receptor beta chain V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2602
Polymers12,1561
Non-polymers1041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.423, 116.295, 34.769
Angle α, β, γ (deg.)90.00, 110.17, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein T-cell receptor beta chain V


Mass: 12156.431 Da / Num. of mol.: 2 / Mutation: G17E, S54N, K66E, Q72H, E80V, L81S, T87S, G96V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: A2NAI0
#2: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID / Malonic acid


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 3.1 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.0 M Sodium Malonate, 0.2 % dioxane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 10, 2003 / Details: mirrors
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→34.4 Å / Num. all: 20008 / Num. obs: 18476 / % possible obs: 92.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4
Reflection shellResolution: 2→2.05 Å / % possible all: 65.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT1.7data extraction
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→34.4 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.828 / SU ML: 0.103 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The residues Gly 63 and Tyr 65 of chain B should be linked according to the sequence database reference. However the C-N bond distance is 2.00 A
RfactorNum. reflection% reflectionSelection details
Rfree0.21 960 5.2 %RANDOM
Rwork0.175 ---
all0.177 20008 --
obs0.177 18476 92.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.722 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å2-0.53 Å2
2---0.96 Å20 Å2
3---0.7 Å2
Refinement stepCycle: LAST / Resolution: 2→34.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1662 0 7 95 1764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211704
X-RAY DIFFRACTIONr_angle_refined_deg1.8791.9342309
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.815212
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.36923.5978
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.69915254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6681510
X-RAY DIFFRACTIONr_chiral_restr0.1480.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021320
X-RAY DIFFRACTIONr_nbd_refined0.2790.2601
X-RAY DIFFRACTIONr_nbtor_refined0.3160.21119
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2109
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.214
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.27
X-RAY DIFFRACTIONr_mcbond_it1.2711.51092
X-RAY DIFFRACTIONr_mcangle_it2.20121706
X-RAY DIFFRACTIONr_scbond_it3.5813696
X-RAY DIFFRACTIONr_scangle_it5.4824.5603
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 50 -
Rwork0.283 922 -
all-972 -
obs--65.37 %

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