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- PDB-4nki: Crystal structure of a Fab -

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Basic information

Entry
Database: PDB / ID: 4nki
TitleCrystal structure of a Fab
Components
  • Fab heavy chainFragment antigen-binding
  • Fab light chainFragment antigen-binding
KeywordsCYTOKINE / nonoclonal antibody / immunoglobulin / antibody / PD-L1 / Soluble protein
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsJiang, X.
CitationJournal: J.Mol.Recognit. / Year: 2015
Title: Epitope characterization of an anti-PD-L1 antibody using orthogonal approaches.
Authors: Hao, G. / Wesolowski, J.S. / Jiang, X. / Lauder, S. / Sood, V.D.
History
DepositionNov 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab light chain
L: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6364
Polymers47,5122
Non-polymers1242
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-24 kcal/mol
Surface area19770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.944, 115.944, 78.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Antibody Fab light chain / Fragment antigen-binding


Mass: 24685.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody Fab heavy chain / Fragment antigen-binding


Mass: 22826.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.81 Å3/Da / Density % sol: 56.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: The crystals were grown using hanging-drop vapor diffusion at 20 C by mixing equal volumes of the purified protein and the crystallization condition of 0.2M lithium sulfate monohydrate and ...Details: The crystals were grown using hanging-drop vapor diffusion at 20 C by mixing equal volumes of the purified protein and the crystallization condition of 0.2M lithium sulfate monohydrate and 20% (wt/vol) polyethylene glycol 3350. , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 12, 2011
RadiationMonochromator: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.41→34.709 Å / Num. obs: 20258

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
BUSTER2.11.5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→34.71 Å / Cor.coef. Fo:Fc: 0.9451 / Cor.coef. Fo:Fc free: 0.9184 / SU B: 33.841 / SU ML: 0.313 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.676 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2449 1097 5.14 %RANDOM
Rwork0.1974 ---
obs0.1998 20258 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.4653 Å20 Å20 Å2
2--0.4653 Å20 Å2
3----0.9306 Å2
Refine analyzeLuzzati coordinate error obs: 0.338 Å
Refinement stepCycle: LAST / Resolution: 2.41→34.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3220 0 8 136 3364
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013305HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.234504HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1070SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes58HARMONIC2
X-RAY DIFFRACTIONt_gen_planes486HARMONIC5
X-RAY DIFFRACTIONt_it3305HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 2.41→2.53 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2544 136 4.86 %
Rwork0.2362 2662 -
all0.2372 2798 -
obs--99.99 %
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)
11.15940.4237-0.6171.0515-0.32791.31840.01840.10010.10910.01640.0427-0.0487-0.0955-0.1482-0.0611-0.14430.0205-0.03290.0569-0.0068-0.153514.482257.57694.5704
22.75910.2887-0.82681.4877-0.21020.5706-0.12830.0082-0.1156-0.26410.0649-0.19420.1290.02230.0634-0.09380.005-0.0745-0.0844-0.0149-0.202627.010145.33548.4559
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ H|* }H1 - 221
2X-RAY DIFFRACTION2{ L|* }L2 - 213

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