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- PDB-2hff: Crystal structure of CB2 Fab -

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Basic information

Entry
Database: PDB / ID: 2hff
TitleCrystal structure of CB2 Fab
Components
  • CB2 Fab, heavy chain
  • CB2 Fab, light chain
KeywordsIMMUNE SYSTEM / fab fragment / phage libraries / combinatorial selection
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHymowitz, S.G.
CitationJournal: Blood / Year: 2006
Title: Synthetic anti-BR3 antibodies that mimic BAFF binding and target both human and murine B cells.
Authors: Lee, C.V. / Hymowitz, S.G. / Wallweber, H.J. / Gordon, N.C. / Billeci, K.L. / Tsai, S.P. / Compaan, D.M. / Yin, J. / Gong, Q. / Kelley, R.F. / Deforge, L.E. / Martin, F. / Starovasnik, M.A. / Fuh, G.
History
DepositionJun 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CB2 Fab, light chain
B: CB2 Fab, heavy chain
L: CB2 Fab, light chain
H: CB2 Fab, heavy chain


Theoretical massNumber of molelcules
Total (without water)95,4404
Polymers95,4404
Non-polymers00
Water2,702150
1
A: CB2 Fab, light chain
B: CB2 Fab, heavy chain


Theoretical massNumber of molelcules
Total (without water)47,7202
Polymers47,7202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-23 kcal/mol
Surface area19020 Å2
MethodPISA
2
L: CB2 Fab, light chain
H: CB2 Fab, heavy chain


Theoretical massNumber of molelcules
Total (without water)47,7202
Polymers47,7202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3270 Å2
ΔGint-21 kcal/mol
Surface area18870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.710, 72.985, 89.919
Angle α, β, γ (deg.)109.42, 100.96, 96.10
Int Tables number1
Space group name H-MP1
DetailsThe crysatllographic assymmetric unit contains two biologically relevant assemblies composed of chains A,B and H,L respectively

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Components

#1: Antibody CB2 Fab, light chain


Mass: 23293.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: protein selected by phage display / Cell line (production host): 4B8 / Production host: Escherichia coli (E. coli)
#2: Antibody CB2 Fab, heavy chain


Mass: 24426.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: protein selected by phage display / Cell line (production host): 4B8 / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.42 Å3/Da / Density % sol: 49.21 %
Crystal growDetails: Crystals were grown in hanging drops with 1:1 ratio of protein to well solution consisting of 100 mM Hepes, pH 7.5, 20% PEG 10K, and then frozen in mother liquor with 25% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9804
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jun 12, 2004
RadiationMonochromator: DOUBLE CRYSTAL SAGITTALLY FOCUSED MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9804 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 63805 / Num. obs: 63805 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rsym value: 0.074 / Net I/σ(I): 6.9
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 6014 / Rsym value: 0.366 / % possible all: 91.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: chains A,B from pdb 2HG9

2hg9


Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 7.739 / SU ML: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22079 6425 10.1 %RANDOM
Rwork0.18907 ---
all0.19229 63790 --
obs0.19229 57365 97.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.246 Å2
Baniso -1Baniso -2Baniso -3
1-1.36 Å20.33 Å20 Å2
2--0.1 Å20.57 Å2
3----1.02 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6389 0 0 150 6539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226535
X-RAY DIFFRACTIONr_bond_other_d0.0010.025725
X-RAY DIFFRACTIONr_angle_refined_deg1.1921.9528900
X-RAY DIFFRACTIONr_angle_other_deg0.721313408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0215842
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.66724.372247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.204151026
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3081526
X-RAY DIFFRACTIONr_chiral_restr0.0740.21019
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027284
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021268
X-RAY DIFFRACTIONr_nbd_refined0.1850.2949
X-RAY DIFFRACTIONr_nbd_other0.180.25289
X-RAY DIFFRACTIONr_nbtor_refined0.1720.22994
X-RAY DIFFRACTIONr_nbtor_other0.080.23994
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2208
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2330.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4190.25
X-RAY DIFFRACTIONr_mcbond_it2.6162.55387
X-RAY DIFFRACTIONr_mcbond_other0.4712.51725
X-RAY DIFFRACTIONr_mcangle_it3.33156835
X-RAY DIFFRACTIONr_scbond_it2.4622.52748
X-RAY DIFFRACTIONr_scangle_it3.51952065
LS refinement shellResolution: 1.95→1.99 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.275 324 -
Rwork0.233 2938 -
obs-2938 84.14 %
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)
11.2399-0.69531.23772.6145-2.07036.0470.02220.1704-0.0151-0.171-0.084-0.03520.08550.13850.0618-0.0448-0.0065-0.0032-0.09070.0005-0.12825.6325-9.0664-15.0378
21.1331-0.01750.17444.90681.51323.97850.10580.02140.1288-0.04490.0181-0.166-0.1260.022-0.124-0.15240.0350.0312-0.16830.01890.0175-4.70421.91890.8153
31.1030.23340.0972.31070.33462.3675-0.03350.0221-0.0469-0.26890.006-0.030.0162-0.03460.0275-0.19140.0080.0117-0.1846-0.0118-0.12237.7129-16.69936.088
42.7404-1.17342.11252.833-1.45623.5011-0.015-0.0384-0.02760.02840.23550.3239-0.0491-0.1895-0.2204-0.14160.01630.03-0.15710.01860.003-11.75469.7829.583
52.0718-0.18070.38091.8007-0.89695.5883-0.1233-0.2651-0.06340.19860.02630.003-0.03350.14480.0970.04160.04090.0043-0.03540.0516-0.1193-9.381-32.406945.4477
62.83441.2488-0.35729.6017-5.58258.53640.3803-0.73330.59471.3227-0.09360.6253-1.9370.1934-0.28680.5001-0.16680.14790.3126-0.27920.03980.60211.553454.6155
71.5164-0.5327-0.15343.277-0.13772.2228-0.0279-0.0602-0.09520.2165-0.0939-0.1050.20270.11270.1218-0.1812-0.0224-0.007-0.11550.0184-0.1161-11.2526-23.605224.7486
82.72-0.21931.91912.0267-1.5359.7750.1234-0.36920.33780.2762-0.15260.039-0.5231.21290.0293-0.0472-0.14540.00190.1759-0.0762-0.05077.9358-2.009240.1021
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1092 - 110
2X-RAY DIFFRACTION2AA110 - 212111 - 213
3X-RAY DIFFRACTION3BB1 - 1141 - 126
4X-RAY DIFFRACTION4BB115 - 214127 - 226
5X-RAY DIFFRACTION5LC1 - 1091 - 110
6X-RAY DIFFRACTION6LC110 - 210111 - 211
7X-RAY DIFFRACTION7HD1 - 1141 - 126
8X-RAY DIFFRACTION8HD115 - 213127 - 225

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