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- PDB-4ky1: humanized HP1/2 Fab -

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Basic information

Entry
Database: PDB / ID: 4ky1
Titlehumanized HP1/2 Fab
Components
  • IMMUNOGLOBULIN IGG1 FAB, HEAVY CHAIN
  • IMMUNOGLOBULIN IGG1 FAB, LIGHT CHAIN
KeywordsIMMUNE SYSTEM / Fab / antibody / alpha4 integrin
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.97 Å
AuthorsArndt, J.W. / Hanf, K.J.M. / Lugovskoy, A. / Chen, L.L. / Jarpe, M. / Boriack-Sjodin, A. / Li, Y. / van Vlijmen, H. / Pepinsky, B. / Taylor, F. ...Arndt, J.W. / Hanf, K.J.M. / Lugovskoy, A. / Chen, L.L. / Jarpe, M. / Boriack-Sjodin, A. / Li, Y. / van Vlijmen, H. / Pepinsky, B. / Taylor, F. / Silvian, L. / Taveras, A.
CitationJournal: METHODS (SAN DIEGO) / Year: 2014
Title: Antibody humanization by redesign of complementarity-determining region residues proximate to the acceptor framework.
Authors: Hanf, K.J. / Arndt, J.W. / Chen, L.L. / Jarpe, M. / Boriack-Sjodin, P.A. / Li, Y. / van Vlijmen, H.W. / Pepinsky, R.B. / Simon, K.J. / Lugovskoy, A.
History
DepositionMay 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Database references
Revision 1.2Sep 20, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: IMMUNOGLOBULIN IGG1 FAB, LIGHT CHAIN
H: IMMUNOGLOBULIN IGG1 FAB, HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)46,7452
Polymers46,7452
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-25 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.010, 100.902, 140.188
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Antibody IMMUNOGLOBULIN IGG1 FAB, LIGHT CHAIN


Mass: 23367.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: muHP1/2 CDRs + human kappa B3 germline VL framework
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO cell / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody IMMUNOGLOBULIN IGG1 FAB, HEAVY CHAIN


Mass: 23377.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: human heavy IGHV1-f germline VH framework + human kappa subgroup 2 consensus VL FW4 region + human heavy subgroup 1 consensus VH FW4 region + human CH1 + human CL1) + VH V24S,F27Y,T32V
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO cell / Production host: Cricetulus griseus (Chinese hamster)

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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: 3.1 Å3/Da / Density % sol: 60.35 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 23% PEG 3350 and 0.2 M ammoniumsulfate, VAPOR DIFFUSION, HANGING DROP, temperature 297K, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.97→50 Å / Num. obs: 12244 / % possible obs: 99.8 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.119 / Χ2: 0.866 / Net I/σ(I): 6.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3-3.1110.50.41812010.521198.9
3.11-3.2310.90.29211940.5531100
3.23-3.38110.21211950.6171100
3.38-3.5611.10.15612180.7641100
3.56-3.78110.1412041.011100
3.78-4.0711.10.1212270.9271100
4.07-4.48110.09612091.1441100
4.48-5.13110.07412460.9961100
5.13-6.4610.90.07112451.0181100
6.46-50100.08513051.082199.5

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FZU

3fzu


Resolution: 2.97→36.66 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.848 / Occupancy max: 1 / Occupancy min: 1 / SU B: 38.46 / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.457 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2843 592 4.8 %RANDOM
Rwork0.206 ---
obs0.2097 12232 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 42.48 Å2 / Biso mean: 39.944 Å2 / Biso min: 16.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2--0.61 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.97→36.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3284 0 0 0 3284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223362
X-RAY DIFFRACTIONr_bond_other_d0.0010.022214
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.9544582
X-RAY DIFFRACTIONr_angle_other_deg0.9293.0025443
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5085431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.90825.039129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.10215539
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.795159
X-RAY DIFFRACTIONr_chiral_restr0.0880.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023742
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02636
X-RAY DIFFRACTIONr_nbd_refined0.2230.2620
X-RAY DIFFRACTIONr_nbd_other0.20.22181
X-RAY DIFFRACTIONr_nbtor_refined0.1920.21577
X-RAY DIFFRACTIONr_nbtor_other0.0940.21867
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.257
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1960.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.21
X-RAY DIFFRACTIONr_mcbond_it0.5191.52720
X-RAY DIFFRACTIONr_mcbond_other0.0791.5871
X-RAY DIFFRACTIONr_mcangle_it0.67223500
X-RAY DIFFRACTIONr_scbond_it1.13431452
X-RAY DIFFRACTIONr_scangle_it1.6964.51082
LS refinement shellResolution: 2.969→3.046 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 34 -
Rwork0.347 751 -
all-785 -
obs--88.2 %
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)
12.7569-0.88121.78972.80360.97415.8830.0660.4258-0.1032-0.13-0.111-0.02080.32890.66210.0449-0.010.07720.04560.13640.0408-0.0465-9.3942-26.8079-55.8478
25.1352-1.3878-2.82151.33190.14275.1764-0.0562-0.2595-0.0290.09390.06880.0514-0.1703-0.3023-0.0126-0.04650.0122-0.07820.01520.0689-0.0474-14.9905-25.3691-20.067
33.9606-0.47120.17922.76950.08924.6456-0.13640.53130.0922-0.3134-0.0795-0.1111-0.08950.28630.2159-0.0413-0.0294-0.0345-0.15520.0685-0.0236-25.713-12.0579-56.4442
48.5799-0.21940.32533.26820.13753.1851-0.3171-0.74690.52110.38740.3023-0.4645-0.5330.25350.01470.1241-0.0493-0.0292-0.0328-0.06930.0561-13.9802-9.6795-23.1096
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 108
2X-RAY DIFFRACTION2L109 - 213
3X-RAY DIFFRACTION3H2 - 121
4X-RAY DIFFRACTION4H122 - 221

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