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- PDB-2apx: Crystal Structure of the G17E/A52V/S54N/K66E/Q72H/E80V/L81S/T87S/... -

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Basic information

Entry
Database: PDB / ID: 2apx
TitleCrystal Structure of the G17E/A52V/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


: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / 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: 1.8 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 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Nov 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3933
Polymers12,1841
Non-polymers2082
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.528, 74.575, 113.083
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-390-

HOH

21A-403-

HOH

31A-489-

HOH

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Components

#1: Protein T cell receptor beta chain V


Mass: 12184.484 Da / Num. of mol.: 1
Mutation: G17E, A52V, 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


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.8 Å3/Da / Density % sol: 55.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.0 M Sodium Malonate, 0.2 % dioxane, pH 7, 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: Nov 13, 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: 1.44→37.3 Å / Num. all: 25200 / Num. obs: 21554 / % possible obs: 85.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4 / Limit h max: 22 / Limit h min: 0 / Limit k max: 51 / Limit k min: 0 / Limit l max: 78 / Limit l min: 0
Reflection shellResolution: 1.44→1.595 Å / % possible all: 37

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT1.7data extraction
CrystalClear(MSC/RIGAKU)data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.515 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.231 682 5.2 %RANDOM
Rwork0.188 ---
all0.19 13208 --
obs0.189 13080 99.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.017 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å20 Å2
2--0.75 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms833 0 14 190 1037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.021863
X-RAY DIFFRACTIONr_angle_refined_deg1.3531.9421168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7385106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88123.5939
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.00915128
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.232155
X-RAY DIFFRACTIONr_chiral_restr0.0980.2126
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02672
X-RAY DIFFRACTIONr_nbd_refined0.2550.2392
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2556
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2149
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.250
X-RAY DIFFRACTIONr_mcbond_it0.8431.5547
X-RAY DIFFRACTIONr_mcangle_it1.3462855
X-RAY DIFFRACTIONr_scbond_it2.3333359
X-RAY DIFFRACTIONr_scangle_it3.2684.5313
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 44 -
Rwork0.326 881 -
all-925 -
obs--97.88 %

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