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- PDB-3mff: 1F1E8hu TCR -

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Basic information

Entry
Database: PDB / ID: 3mff
Title1F1E8hu TCR
Components(T cell receptor ...) x 2
KeywordsIMMUNE SYSTEM / T-cell receptor / Protein metamorphism / Alpha constant domain
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ARGININE / UREA
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
Authorsvan Boxel, G.I. / Holmes, S. / Fugger, L. / Jones, E.Y.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: An alternative conformation of the T-cell receptor alpha constant region
Authors: van Boxel, G.I. / Holmes, S. / Fugger, L. / Jones, E.Y.
History
DepositionApr 2, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: T cell receptor alpha chain
B: T cell receptor beta chain
C: T cell receptor alpha chain
D: T cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,54710
Polymers100,0074
Non-polymers5406
Water14,448802
1
A: T cell receptor alpha chain
B: T cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1564
Polymers50,0042
Non-polymers1522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-18 kcal/mol
Surface area20690 Å2
MethodPISA
2
C: T cell receptor alpha chain
D: T cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3916
Polymers50,0042
Non-polymers3874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-19 kcal/mol
Surface area21140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.323, 74.016, 94.267
Angle α, β, γ (deg.)90.00, 91.59, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALSERSER5AA12 - 2102 - 200
21VALVALSERSER5CC12 - 2102 - 200
12LYSLYSTRPTRP4BB3 - 2402 - 239
22LYSLYSTRPTRP4DD3 - 2402 - 239

NCS ensembles :
ID
1
2

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Components

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T cell receptor ... , 2 types, 4 molecules ACBD

#1: Protein T cell receptor alpha chain


Mass: 22338.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET 22d / Production host: Escherichia coli (E. coli) / Strain (production host): JM22
#2: Protein T cell receptor beta chain


Mass: 27664.912 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET 22d / Production host: Escherichia coli (E. coli) / Strain (production host): JM22

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Non-polymers , 4 types, 808 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH4N2O
#5: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 802 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsSEQUENCE DATABASE REFERENCE FOR BOTH ENTITIES DO NOT CURRENTLY EXIST.

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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: 3.04 Å3/Da / Density % sol: 59.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.3mM (NH4)2HydrogenCitrate, 20%(w/v) PEG3000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.983 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 19, 2004 / Details: mirrors
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.983 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 74855 / % possible obs: 91.7 % / Observed criterion σ(F): 0.951 / Observed criterion σ(I): 0.953 / Redundancy: 9.2 % / Biso Wilson estimate: 36.8 Å2 / Rmerge(I) obs: 0.2 / Rsym value: 0.051 / Net I/σ(I): 20.2
Reflection shellResolution: 2→2.052 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 0.284 / Num. unique all: 3611 / Rsym value: 0.259 / % possible all: 63.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.2.0005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 1 / SU B: 8.061 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.185 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24293 3772 5.1 %RANDOM
Rwork0.19988 ---
all0.243 ---
obs0.20203 70789 91.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.61 Å2 / Biso mean: 36.816 Å2 / Biso min: 14.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å22.27 Å2
2---0.79 Å20 Å2
3---1.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.04 Å0.03 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6947 0 35 802 7784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227162
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.949721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8755867
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70924.221353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.425151154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9161542
X-RAY DIFFRACTIONr_chiral_restr0.1060.21032
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025566
X-RAY DIFFRACTIONr_nbd_refined0.2180.23184
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24769
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2714
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.245
X-RAY DIFFRACTIONr_mcbond_it0.8421.54500
X-RAY DIFFRACTIONr_mcangle_it1.39927070
X-RAY DIFFRACTIONr_scbond_it2.11833077
X-RAY DIFFRACTIONr_scangle_it3.2324.52651
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A760medium positional0.190.5
2B1909medium positional0.330.5
1A733loose positional0.485
1A760medium thermal0.712
2B1909medium thermal0.652
1A733loose thermal1.1510
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 187 -
Rwork0.243 3611 -
obs--63.92 %

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