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- PDB-1h5b: T cell receptor Valpha11 (AV11S5) domain -

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Basic information

Entry
Database: PDB / ID: 1h5b
TitleT cell receptor Valpha11 (AV11S5) domain
Components(MURINE T CELL RECEPTOR (TCR) VALPHA ...) x 3
KeywordsT CELL RECEPTOR / IMMUNE RESPONSE / IMMUNOGLOBULIN FOLD
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsMachius, M. / Cianga, P. / Deisenhofer, J. / Sally Ward, E.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Crystal Structure of a T Cell Receptor Valpha11 (Av11S5) Domain: New Canonical Forms for the First and Second Complementarity Determining Regions
Authors: Machius, M. / Cianga, P. / Deisenhofer, J. / Ward, E.S.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: Canonical Structures for the Hypervariable Regions of T Cell Ab Receptors
Authors: Al-Lazikani, B. / Lesk, A.M.
History
DepositionMay 21, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2001Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Mar 6, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Oct 16, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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: MURINE T CELL RECEPTOR (TCR) VALPHA DOMAIN
B: MURINE T CELL RECEPTOR (TCR) VALPHA DOMAIN
C: MURINE T CELL RECEPTOR (TCR) VALPHA DOMAIN
D: MURINE T CELL RECEPTOR (TCR) VALPHA DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0728
Polymers49,8734
Non-polymers1984
Water3,873215
1
A: MURINE T CELL RECEPTOR (TCR) VALPHA DOMAIN
B: MURINE T CELL RECEPTOR (TCR) VALPHA DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9784
Polymers24,9072
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: MURINE T CELL RECEPTOR (TCR) VALPHA DOMAIN
D: MURINE T CELL RECEPTOR (TCR) VALPHA DOMAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0934
Polymers24,9662
Non-polymers1282
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)83.531, 83.531, 132.463
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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MURINE T CELL RECEPTOR (TCR) VALPHA ... , 3 types, 4 molecules ABDC

#1: Protein MURINE T CELL RECEPTOR (TCR) VALPHA DOMAIN


Mass: 12432.696 Da / Num. of mol.: 1 / Fragment: V-ALPHA DOMAIN VA85.33 (AV11S5-AJ17)
Source method: isolated from a genetically manipulated source
Details: C-TERMINAL HEXA-HISTIDINE TAG / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: QCII85.33 VALPHAPELBHIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BMH71-18
#2: Protein MURINE T CELL RECEPTOR (TCR) VALPHA DOMAIN


Mass: 12474.799 Da / Num. of mol.: 2 / Fragment: V-ALPHA DOMAIN VA85.33 (AV11S5-AJ17)
Source method: isolated from a genetically manipulated source
Details: C-TERMINAL HEXA-HISTIDINE TAG / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: QCII85.33 VALPHAPELBHIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BMH71-18
#3: Protein MURINE T CELL RECEPTOR (TCR) VALPHA DOMAIN


Mass: 12490.799 Da / Num. of mol.: 1 / Fragment: V-ALPHA DOMAIN VA85.33 (AV11S5-AJ17)
Source method: isolated from a genetically manipulated source
Details: C-TERMINAL HEXA-HISTIDINE TAG / Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: QCII85.33 VALPHAPELBHIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BMH71-18

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Non-polymers , 3 types, 219 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.7 Å3/Da / Density % sol: 54.1 % / Description: SPOTS HAD SMEARY APPEARANCE AT HIGH RESOLUTION
Crystal growMethod: vapor diffusion / pH: 5.5
Details: 20C, VAPOR DIFFUSION, 3 UL PROTEIN (5 MG/ML IN 50 MM TRIS/CL, 100 MM NACL, PH 8.0) + 3 UL RESERVOIR SOLUTION (100 MM SODIUM CITRATE/HCL, 1.4-1.7 M LITHIUM CHLORIDE, PH 5.0-6.0) EQUILIBRATED ...Details: 20C, VAPOR DIFFUSION, 3 UL PROTEIN (5 MG/ML IN 50 MM TRIS/CL, 100 MM NACL, PH 8.0) + 3 UL RESERVOIR SOLUTION (100 MM SODIUM CITRATE/HCL, 1.4-1.7 M LITHIUM CHLORIDE, PH 5.0-6.0) EQUILIBRATED AGAINST 1 ML OF RESERVOIR SOLUTION.
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
250 mMTris-HCl1drop
3100 mM1dropNaCl
4100 mMsodium citrate-HCl1reservoir
51.4-1.7 M1reservoirLiCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793
DetectorType: APS1 / Detector: CCD / Date: Feb 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.85→72.34 Å / Num. obs: 45847 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 30.8
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 3.1 / % possible all: 97.9
Reflection shell
*PLUS
% possible obs: 97.9 %

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.85→39.83 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1253020.99 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2189 5 %RANDOM
Rwork0.224 ---
obs0.224 43980 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 67.5957 Å2 / ksol: 0.385249 e/Å3
Displacement parametersBiso mean: 39.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.94 Å20.2 Å20 Å2
2--1.94 Å20 Å2
3----3.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.85→39.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3474 0 9 215 3698
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.62
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.761.5
X-RAY DIFFRACTIONc_mcangle_it2.982
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it3.242.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.305 317 4.8 %
Rwork0.273 6317 -
obs--87.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4MY_GLYCEROL.PARAMMY_GLYCEROL.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.62

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