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- PDB-4hk3: I2 Fab (unbound) from CH65-CH67 Lineage -

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Basic information

Entry
Database: PDB / ID: 4hk3
TitleI2 Fab (unbound) from CH65-CH67 Lineage
Components
  • I2 heavy chain
  • I2 light chain
KeywordsIMMUNE SYSTEM / Fab fragment
Function / homology
Function and homology information


Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsSchmidt, A.G. / Harrison, S.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Preconfiguration of the antigen-binding site during affinity maturation of a broadly neutralizing influenza virus antibody.
Authors: Schmidt, A.G. / Xu, H. / Khan, A.R. / O'Donnell, T. / Khurana, S. / King, L.R. / Manischewitz, J. / Golding, H. / Suphaphiphat, P. / Carfi, A. / Settembre, E.C. / Dormitzer, P.R. / Kepler, T. ...Authors: Schmidt, A.G. / Xu, H. / Khan, A.R. / O'Donnell, T. / Khurana, S. / King, L.R. / Manischewitz, J. / Golding, H. / Suphaphiphat, P. / Carfi, A. / Settembre, E.C. / Dormitzer, P.R. / Kepler, T.B. / Zhang, R. / Moody, M.A. / Haynes, B.F. / Liao, H.X. / Shaw, D.E. / Harrison, S.C.
History
DepositionOct 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
J: I2 heavy chain
N: I2 light chain


Theoretical massNumber of molelcules
Total (without water)48,4682
Polymers48,4682
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-24 kcal/mol
Surface area19950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.455, 102.455, 81.492
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

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Components

#1: Antibody I2 heavy chain


Mass: 25771.789 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#2: Antibody I2 light chain


Mass: 22695.977 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: Q8N355*PLUS

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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: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.5 M sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99997 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 29, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 2.498→50 Å / Num. all: 16978 / Num. obs: 16968 / % possible obs: 100 % / Redundancy: 15 % / Rmerge(I) obs: 0.06 / Χ2: 0.713 / Net I/σ(I): 8.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→38.964 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7724 / SU ML: 0.35 / σ(F): 1.38 / Phase error: 29.41 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2896 494 5.02 %
Rwork0.2206 --
obs0.2239 9841 99.9 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.11 Å2 / ksol: 0.313 e/Å3
Displacement parametersBiso max: 145.95 Å2 / Biso mean: 47.2921 Å2 / Biso min: 5.29 Å2
Baniso -1Baniso -2Baniso -3
1-6.4939 Å2-0 Å2-0 Å2
2--6.4939 Å20 Å2
3----12.9878 Å2
Refinement stepCycle: LAST / Resolution: 3→38.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3234 0 0 0 3234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093342
X-RAY DIFFRACTIONf_angle_d1.2934558
X-RAY DIFFRACTIONf_chiral_restr0.076511
X-RAY DIFFRACTIONf_plane_restr0.007584
X-RAY DIFFRACTIONf_dihedral_angle_d16.2291175
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3-3.30190.33771140.267323242438
3.3019-3.77930.31771380.229723162454
3.7793-4.76020.25771260.193723262452
4.7602-38.96780.27221160.215523812497
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.20290.2355-0.09130.4477-0.19280.1877-0.36530.0489-0.0262-0.439-0.1142-0.53950.16510.1599-0.7476-0.7415-0.91160.7494-1.08750.6837-0.5182-31.550331.749-6.1874
20.04080.0010.03450.02710.03190.0522-0.04190.2611-0.1473-0.1-0.0693-0.06440.06790.14420.00971.07-0.01430.56930.62990.26710.5881-23.65757.002915.9286
30.4225-0.0198-0.14640.03320.04780.4204-0.2008-0.4069-0.1290.1267-0.14720.07120.4966-0.3217-0.4691-0.1419-0.64720.2962-0.15770.413-0.3518-52.329324.7266-2.7558
40.008-0.02920.00630.2914-0.17440.1745-0.221-0.0817-0.1358-0.1955-0.1471-0.4074-0.0060.1594-0.00790.75380.29670.29030.49020.1710.5619-32.65087.826.4808
50.0892-0.0040.04350.11630.04940.1452-0.1425-0.0249-0.0937-0.3744-0.2156-0.256-0.0351-0.0074-0.33790.64840.26950.29220.40670.66410.3937-36.46239.152629.1341
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'J' and (resseq 1:126)J1 - 126
2X-RAY DIFFRACTION2chain 'J' and (resseq 127:227)J127 - 227
3X-RAY DIFFRACTION3chain 'N' and (resseq 1:115)N1 - 115
4X-RAY DIFFRACTION4chain 'N' and (resseq 116:152)N116 - 152
5X-RAY DIFFRACTION5chain 'N' and (resseq 153:210)N153 - 210

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