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- PDB-5i8k: HHH1 Fab fragment -

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Basic information

Entry
Database: PDB / ID: 5i8k
TitleHHH1 Fab fragment
Components
  • HHH1 Fab Heavy chain
  • HHH1 Fab Light chain
KeywordsIMMUNE SYSTEM / antibody / glycan binding / Fab / allergy
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.771 Å
AuthorsAndersen, G.R. / Spillner, E.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk Foundation Denmark
CitationJournal: To be published
Title: HHH1 Fab fragment
Authors: Tjerrild, L.M. / Andersen, G.R. / Spillner, E.
History
DepositionFeb 19, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
L: HHH1 Fab Light chain
H: HHH1 Fab Heavy chain


Theoretical massNumber of molelcules
Total (without water)46,4492
Polymers46,4492
Non-polymers00
Water9,800544
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-29 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.647, 62.647, 227.891
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Antibody HHH1 Fab Light chain


Mass: 23377.797 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#2: Antibody HHH1 Fab Heavy chain


Mass: 23070.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 544 / 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: 2.44 Å3/Da / Density % sol: 49.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 15-19% (v/v) Isopropanol, 15-24.5% (w/v) PEG 3350, 0.075 M MES pH 5.5-6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Aug 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.77→48.331 Å / Num. obs: 45033 / % possible obs: 99.21 % / Redundancy: 10.16 % / Rsym value: 0.077 / Net I/σ(I): 21.15
Reflection shellResolution: 1.77→1.83 Å

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MA3 with CDR regions removed

4ma3


Resolution: 1.771→48.331 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.46
RfactorNum. reflection% reflectionSelection details
Rfree0.2115 2259 5.02 %5% random
Rwork0.1827 ---
obs0.1842 45031 99.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.01 Å2 / Biso mean: 25.6256 Å2 / Biso min: 8.8 Å2
Refinement stepCycle: final / Resolution: 1.771→48.331 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3222 0 0 544 3766
Biso mean---35.7 -
Num. residues----434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053303
X-RAY DIFFRACTIONf_angle_d0.9824500
X-RAY DIFFRACTIONf_chiral_restr0.038520
X-RAY DIFFRACTIONf_plane_restr0.005573
X-RAY DIFFRACTIONf_dihedral_angle_d11.7981149
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.771-1.80950.29871360.2922332246889
1.8095-1.85160.30421370.25692626276398
1.8516-1.89790.25511410.238426212762100
1.8979-1.94920.24811460.201926192765100
1.9492-2.00660.21561390.186426432782100
2.0066-2.07140.22021390.185326422781100
2.0714-2.14540.21091480.177626512799100
2.1454-2.23130.22011530.177526692822100
2.2313-2.33290.19751420.179126632805100
2.3329-2.45580.2291480.178426602808100
2.4558-2.60970.20661380.181627122850100
2.6097-2.81120.21341220.183827022824100
2.8112-3.0940.24011430.186227052848100
3.094-3.54160.19351400.178227552895100
3.5416-4.46160.18511380.156828032941100
4.4616-48.34940.18391490.176329693118100
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)
11.6821-0.48130.84180.6048-0.35731.830.0543-0.1269-0.13680.072-0.010700.06650.0167-0.04540.1310.0015-0.00840.11530.01180.12049.2466-16.86549.8608
22.0025-0.0665-0.17790.4201-0.67732.64490.1324-0.23240.23850.0031-0.0296-0.18520.01840.6977-0.09270.1433-0.01480.0070.3078-0.04190.230929.1638-9.72795.825
31.2680.115-1.02660.72490.21353.0249-0.03910.0773-0.0097-0.10990.0146-0.01110.0756-0.00970.01740.12410.00680.00810.0907-0.00820.11976.2736-10.284-27.0276
43.4497-0.7847-0.04111.8318-0.14541.73090.01870.15350.0264-0.0547-0.0855-0.0121-0.05830.03960.05580.1162-0.01380.00540.093-0.00120.112813.69731.7175-20.4927
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'L' and resid 2 through 112)L2 - 112
2X-RAY DIFFRACTION2(chain 'H' and resid 2 through 116)H2 - 116
3X-RAY DIFFRACTION3(chain 'L' and resid 113 through 217)L113 - 217
4X-RAY DIFFRACTION4(chain 'H' and resid 117 through 219)H117 - 219

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