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- PDB-3mj8: Crystal structure of HL4E10 Fab, a hamster Ab stimulatory for gam... -

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Basic information

Entry
Database: PDB / ID: 3mj8
TitleCrystal structure of HL4E10 Fab, a hamster Ab stimulatory for gammadelta T cells
Components
  • STIMULATORY HAMSTER ANTIBODY HL4E10 FAB HEAVY CHAIN
  • STIMULATORY HAMSTER ANTIBODY HL4E10 FAB LIGHT CHAIN
KeywordsIMMUNE SYSTEM / ANTIBODY / HAMSTER IgG
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesCRICETULUS MIGRATORIUS (Armenian hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsVerdino, P. / Wilson, I.A.
CitationJournal: Plos One / Year: 2011
Title: cDNA sequence and Fab crystal structure of HL4E10, a hamster IgG lambda light chain antibody stimulatory for gammadelta T cells.
Authors: Verdino, P. / Witherden, D.A. / Podshivalova, K. / Rieder, S.E. / Havran, W.L. / Wilson, I.A.
History
DepositionApr 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 5, 2013Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: STIMULATORY HAMSTER ANTIBODY HL4E10 FAB LIGHT CHAIN
H: STIMULATORY HAMSTER ANTIBODY HL4E10 FAB HEAVY CHAIN
A: STIMULATORY HAMSTER ANTIBODY HL4E10 FAB LIGHT CHAIN
B: STIMULATORY HAMSTER ANTIBODY HL4E10 FAB HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)92,8764
Polymers92,8764
Non-polymers00
Water00
1
L: STIMULATORY HAMSTER ANTIBODY HL4E10 FAB LIGHT CHAIN
H: STIMULATORY HAMSTER ANTIBODY HL4E10 FAB HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)46,4382
Polymers46,4382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-28 kcal/mol
Surface area19960 Å2
MethodPISA
2
A: STIMULATORY HAMSTER ANTIBODY HL4E10 FAB LIGHT CHAIN
B: STIMULATORY HAMSTER ANTIBODY HL4E10 FAB HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)46,4382
Polymers46,4382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-29 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.836, 148.768, 68.798
Angle α, β, γ (deg.)90.00, 106.23, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21A
12H
22B

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERPROPROLA1 - 2111 - 209
21SERSERPROPROAC1 - 2111 - 209
12GLNGLNGLYGLYHB1 - 2281 - 218
22GLNGLNGLYGLYBD1 - 2281 - 218

NCS ensembles :
ID
1
2

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Components

#1: Antibody STIMULATORY HAMSTER ANTIBODY HL4E10 FAB LIGHT CHAIN


Mass: 22784.334 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: HL4E10-SECRETING HYBRIDOMA WAS PRODUCED BY FUSING MOUSE MYELOMA CELLS WITH SPLEEN CELLS FROM AN ARMENIAN HAMSTER IMMUNIZED WITH 7-17 DETC
Source: (natural) CRICETULUS MIGRATORIUS (Armenian hamster) / Strain: HYBRIDOMA
#2: Antibody STIMULATORY HAMSTER ANTIBODY HL4E10 FAB HEAVY CHAIN


Mass: 23653.455 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: HL4E10-SECRETING HYBRIDOMA WAS PRODUCED BY FUSING MOUSE MYELOMA CELLS WITH SPLEEN CELLS FROM AN ARMENIAN HAMSTER IMMUNIZED WITH 7-17 DETC
Source: (natural) CRICETULUS MIGRATORIUS (Armenian hamster) / Strain: HYBRIDOMA
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: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 10-12.5 % PEG 4000, 0.1 M NA- ACETATE, 0.2 M (NH4)2SO4, pH 4.60, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97946
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 12, 2006
Details: FLAT MIRROR (VERTICAL FOCUSING), SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING)
RadiationMonochromator: SIDE SCATTERING BENT CUBE- ROOT I-BEAM SINGLE CRYSTAL, ASYMMETRIC CUT 4.965 DEGS
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.94→30 Å / Num. obs: 17012 / % possible obs: 95.3 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 70.8 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 7.7
Reflection shellResolution: 2.94→3.06 Å / Rmerge(I) obs: 0.541 / Mean I/σ(I) obs: 1.7 / Rsym value: 0.541 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.3.0017refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HL4E10 LIGHT CHAIN SEQUENCE THREADED ONTO 1W72, HL4E10 HEAVY CHAIN SEQUENCE THREADED ONTO 2ARJ

1w72

2arj


Resolution: 2.94→30 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.869 / SU B: 56.081 / SU ML: 0.457 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.536 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CNS WAS ALSO USED FOR THE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.281 863 5.1 %RANDOM
Rwork0.227 ---
obs0.23 16120 94.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 54.67 Å2
Baniso -1Baniso -2Baniso -3
1-4.15 Å20 Å2-2.78 Å2
2---1.05 Å20 Å2
3----4.65 Å2
Refinement stepCycle: LAST / Resolution: 2.94→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6320 0 0 0 6320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226488
X-RAY DIFFRACTIONr_bond_other_d0.0010.024198
X-RAY DIFFRACTIONr_angle_refined_deg0.9571.9438874
X-RAY DIFFRACTIONr_angle_other_deg0.7443.00310324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7665834
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.77524.831236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.29815990
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2741514
X-RAY DIFFRACTIONr_chiral_restr0.0560.21022
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.027206
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021220
X-RAY DIFFRACTIONr_nbd_refined0.1780.21204
X-RAY DIFFRACTIONr_nbd_other0.1710.24054
X-RAY DIFFRACTIONr_nbtor_refined0.1730.23030
X-RAY DIFFRACTIONr_nbtor_other0.0790.23563
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2134
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1250.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1310.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1481.55336
X-RAY DIFFRACTIONr_mcbond_other0.0211.51692
X-RAY DIFFRACTIONr_mcangle_it0.18426786
X-RAY DIFFRACTIONr_scbond_it0.25932800
X-RAY DIFFRACTIONr_scangle_it0.3954.52088
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1L2619medium positional0.420.5
2H2640medium positional0.470.5
1L2619medium thermal0.12
2H2640medium thermal0.092
LS refinement shellResolution: 2.94→3.02 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.546 56 -
Rwork0.38 1063 -
obs--86.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.3963-0.97843.05157.3807-3.99168.597-0.00770.09470.277-0.51210.20060.78230.2407-0.5352-0.1929-0.1805-0.1556-0.0035-0.0318-0.0165-0.065-7.5799-1.4292-5.1741
22.43742.33342.318511.79417.621910.40150.1212-0.3440.18460.3072-0.37450.9051-0.0268-0.80070.2533-0.3499-0.12040.0804-0.02110.075-0.05432.04867.233327.7858
33.18061.45931.08875.80331.67686.8508-0.47560.2410.3263-0.38690.24420.4483-1.0088-0.13270.2314-0.0162-0.0189-0.1099-0.08660.0854-0.0437-0.886619.3738-8.6858
42.1562-0.45381.4869.35660.02728.12280.123-0.2305-0.34820.1233-0.2125-0.49580.36040.29620.0895-0.1965-0.19860.0747-0.0897-0.0575-0.082417.006812.929224.413
53.68073.0177-1.85096.3238-2.109411.30080.0575-0.23360.33950.8723-0.14790.2522-0.61690.12840.0904-0.050.0412-0.0812-0.25980.0054-0.040417.9138-18.6505-27.4788
67.68952.76392.8883.41662.87815.9611-0.1316-0.16410.4559-0.0503-0.28190.3584-0.7956-1.05990.4135-0.10340.02220.02590.1327-0.0278-0.0569-1.7947-20.9638-57.3275
73.24631.17281.12192.7988-2.24438.7017-0.0035-0.0761-0.12740.16140.19660.3450.3601-1.0761-0.19310.0483-0.05050.1311-0.050.0208-0.05435.341-35.8577-21.7836
85.09761.1156-0.31892.08360.45298.25240.3046-0.1799-0.2862-0.0189-0.40480.07820.371-0.55520.10020.0143-0.0631-0.036-0.1246-0.0189-0.0278-0.0123-36.963-59.3793
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 108
2X-RAY DIFFRACTION2L109 - 211
3X-RAY DIFFRACTION3H1 - 113
4X-RAY DIFFRACTION4H114 - 228
5X-RAY DIFFRACTION5A1 - 108
6X-RAY DIFFRACTION6A109 - 211
7X-RAY DIFFRACTION7B1 - 113
8X-RAY DIFFRACTION8B114 - 228

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