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- PDB-3hc0: BHA10 IgG1 wild-type Fab - antibody directed at human LTBR -

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Basic information

Entry
Database: PDB / ID: 3hc0
TitleBHA10 IgG1 wild-type Fab - antibody directed at human LTBR
Components
  • IMMUNOGLOBULIN IGG1 FAB, HEAVY CHAIN
  • IMMUNOGLOBULIN IGG1 FAB, LIGHT CHAIN
KeywordsIMMUNE SYSTEM / IGG1 FAB / BHA10
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsArndt, J.W. / Jordan, J.L. / Lugovskoy, A. / Wang, D.
CitationJournal: Proteins / Year: 2009
Title: Structural understanding of stabilization patterns in engineered bispecific Ig-like antibody molecules
Authors: Jordan, J.L. / Arndt, J.W. / Hanf, K. / Li, G. / Hall, J. / Demarest, S. / Huang, F. / Wu, X. / Miller, B. / Glaser, S. / Fernandez, E.J. / Wang, D. / Lugovskoy, A.
History
DepositionMay 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: IMMUNOGLOBULIN IGG1 FAB, LIGHT CHAIN
L: IMMUNOGLOBULIN IGG1 FAB, HEAVY CHAIN
A: IMMUNOGLOBULIN IGG1 FAB, LIGHT CHAIN
B: IMMUNOGLOBULIN IGG1 FAB, HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3566
Polymers93,2384
Non-polymers1182
Water7,350408
1
H: IMMUNOGLOBULIN IGG1 FAB, LIGHT CHAIN
L: IMMUNOGLOBULIN IGG1 FAB, HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6783
Polymers46,6192
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-25 kcal/mol
Surface area19490 Å2
MethodPISA
2
A: IMMUNOGLOBULIN IGG1 FAB, LIGHT CHAIN
B: IMMUNOGLOBULIN IGG1 FAB, HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6783
Polymers46,6192
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-25 kcal/mol
Surface area19290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.157, 46.193, 150.628
Angle α, β, γ (deg.)90.00, 96.48, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody IMMUNOGLOBULIN IGG1 FAB, LIGHT CHAIN


Mass: 23356.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: CHINESE HAMSTER OVARY / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody IMMUNOGLOBULIN IGG1 FAB, HEAVY CHAIN


Mass: 23262.705 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: CHINESE HAMSTER OVARY / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 408 / Source method: isolated from a natural source / Formula: H2O

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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: 2.58 Å3/Da / Density % sol: 52.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 22% PEG 4000, 100 mM calcium acetate and 100 mM Tris at pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2008
RadiationMonochromator: DIAMOND(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 76203 / % possible obs: 96.2 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.064
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.373 / % possible all: 88.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.552 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.143 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.206 3683 5 %RANDOM
Rwork0.18 ---
obs0.182 69586 96.2 %-
all-76203 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å2-0.17 Å2
2---0.76 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6474 0 8 408 6890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226697
X-RAY DIFFRACTIONr_bond_other_d0.0070.024452
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.9469125
X-RAY DIFFRACTIONr_angle_other_deg0.8633.00210901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9715851
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06224.487263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.861151056
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8741520
X-RAY DIFFRACTIONr_chiral_restr0.0850.21013
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027496
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021328
X-RAY DIFFRACTIONr_nbd_refined0.210.2983
X-RAY DIFFRACTIONr_nbd_other0.2090.24353
X-RAY DIFFRACTIONr_nbtor_refined0.1770.23161
X-RAY DIFFRACTIONr_nbtor_other0.0870.23577
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2363
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3070.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4011.55400
X-RAY DIFFRACTIONr_mcbond_other0.1821.51715
X-RAY DIFFRACTIONr_mcangle_it1.40426896
X-RAY DIFFRACTIONr_scbond_it2.38632965
X-RAY DIFFRACTIONr_scangle_it3.3354.52229
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 238 -
Rwork0.21 4730 -
obs--88.89 %
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)
11.49740.43770.88640.90710.66831.4733-0.0795-0.03850.0594-0.00990.00370.0637-0.0585-0.07770.0758-0.02810.0006-0.0249-0.0159-0.0023-0.0366-62.38410.36954.674
21.2086-0.5225-0.47982.48640.76631.667-0.0308-0.05080.0171-0.09730.0776-0.2163-0.00750.1319-0.0468-0.063-0.0288-0.0068-0.02460.005-0.0117-27.7754.853.18
31.5754-0.22510.9560.7873-0.3093.0691-0.01210.2681-0.0599-0.0835-0.0049-0.08980.01210.17130.0171-0.0630.0045-0.00290.0806-0.0394-0.0935-5.636-24.8116.652
43.2606-0.9628-1.98472.11791.03544.51260.26570.13450.4134-0.0307-0.07290.031-0.52590.1458-0.19280.0257-0.04160.0205-0.07960.0409-0.0437-31.308-1.94513.348
51.1047-0.5127-0.27070.85890.17330.44980.0291-0.0075-0.05430.0494-0.0270.02190.0461-0.0158-0.0021-0.0257-0.0099-0.0148-0.010.0046-0.0285-60.992-10.95449.221
60.90840.22750.77260.84350.40581.6502-0.0107-0.042-0.00950.03560.0001-0.06780.00850.05920.0107-0.03760.0043-0.0182-0.00470.0116-0.0336-27.936-7.88563.053
72.2106-0.7095-0.17981.00930.3551.05270.07570.0339-0.12820.0029-0.02930.00290.0384-0.079-0.0464-0.0588-0.0344-0.0161-0.0071-0.0101-0.0392-18.56-28.44434.355
81.7118-0.47540.97520.2025-0.77674.18740.10060.12290.009-0.02970.00830.00110.1408-0.1573-0.1090.025-0.0129-0.03180.02060.0171-0.1034-44.78-11.98915.91
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 116
2X-RAY DIFFRACTION2H117 - 217
3X-RAY DIFFRACTION3A1 - 116
4X-RAY DIFFRACTION4A117 - 216
5X-RAY DIFFRACTION5L1 - 108
6X-RAY DIFFRACTION6L109 - 212
7X-RAY DIFFRACTION7B1 - 108
8X-RAY DIFFRACTION8B109 - 212

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