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- PDB-3rev: Crystal structure of human alloreactive tcr nb20 -

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Basic information

Entry
Database: PDB / ID: 3rev
TitleCrystal structure of human alloreactive tcr nb20
Components
  • TCR NB20 ALPHA CHAIN
  • TCR NB20 BETA CHAIN
KeywordsIMMUNE SYSTEM / T CELL RECEPTOR / MHC CLASS I / TUMOUR ANTIGEN / IMMUNE RESPONSE / ALLOREACTIVITY / IMMUNOGLOBULIN DOMAIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWood, A. / Mohammed, F. / Salim, M. / Tranter, A. / Rickinson, A.B. / Moss, P.A.H. / Stauss, H.J. / Steven, N.M. / Willcox, B.E.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural and energetic evidence for highly peptide-specific tumor antigen targeting via allo-MHC restriction.
Authors: Simpson, A.A. / Mohammed, F. / Salim, M. / Tranter, A. / Rickinson, A.B. / Stauss, H.J. / Moss, P.A. / Steven, N.M. / Willcox, B.E.
History
DepositionApr 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 27, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TCR NB20 ALPHA CHAIN
B: TCR NB20 BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6653
Polymers49,6032
Non-polymers621
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-17 kcal/mol
Surface area20330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.240, 72.770, 96.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TCR NB20 ALPHA CHAIN


Mass: 22586.189 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS
#2: Protein TCR NB20 BETA CHAIN


Mass: 27017.014 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 22% PEG 4000, 0.2M AMMONIUM ACETATE, 0.1M CITRIC ACID, PH 4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.979355
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979355 Å / Relative weight: 1
ReflectionResolution: 2.2→66.227 Å / Num. obs: 24266 / % possible obs: 100 % / Redundancy: 6 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 7.949
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 1.4 / % possible all: 100

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Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→58 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1187 4.9 %Random
Rwork0.232 ---
obs0.232 24072 99.4 %-
Solvent computationBsol: 56.36 Å2
Displacement parametersBiso mean: 38 Å2
Baniso -1Baniso -2Baniso -3
1--3.25 Å20 Å20 Å2
2--5.812 Å20 Å2
3----2.561 Å2
Refinement stepCycle: LAST / Resolution: 2.2→58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3478 0 4 124 3606
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3EDO.PARAM

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