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- PDB-4hbc: Crystal structure of a conformation-dependent rabbit IgG Fab spec... -

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Basic information

Entry
Database: PDB / ID: 4hbc
TitleCrystal structure of a conformation-dependent rabbit IgG Fab specific for amyloid prefibrillar oligomers
Components
  • Antigen Binding Fragment, Immunoglobulin IgG - Heavy ChainFragment antigen-binding
  • Antigen Binding Fragment, Immunoglobulin IgG - Light ChainFragment antigen-binding
KeywordsIMMUNE SYSTEM / Fab / rabbit / conformation-specific / amyloid
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.54 Å
AuthorsArai, H.
CitationJournal: Biochim.Biophys.Acta / Year: 2012
Title: Crystal structure of a conformation-dependent rabbit IgG Fab specific for amyloid prefibrillar oligomers.
Authors: Arai, H. / Glabe, C. / Luecke, H.
History
DepositionSep 27, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionOct 31, 2012ID: 3NL4
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Antigen Binding Fragment, Immunoglobulin IgG - Heavy Chain
L: Antigen Binding Fragment, Immunoglobulin IgG - Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4693
Polymers45,3732
Non-polymers961
Water7,819434
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-39 kcal/mol
Surface area18380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.934, 42.184, 86.179
Angle α, β, γ (deg.)90.000, 114.930, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-503-

HOH

21H-511-

HOH

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Components

#1: Antibody Antigen Binding Fragment, Immunoglobulin IgG - Heavy Chain / Fragment antigen-binding


Mass: 22683.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#2: Antibody Antigen Binding Fragment, Immunoglobulin IgG - Light Chain / Fragment antigen-binding


Mass: 22689.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium sulfate 20 % PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979462 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979462 Å / Relative weight: 1
ReflectionResolution: 1.54→31.01 Å / Num. obs: 56536 / % possible obs: 87.6 % / Redundancy: 6.46 % / Rmerge(I) obs: 0.081 / Χ2: 0.96 / Net I/σ(I): 10.2 / Scaling rejects: 2758
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.54-1.64.670.5321492731911.2549.7
1.6-1.6650.4282.52047740761.1763.5
1.66-1.735.580.3553.22822550501.1478.9
1.73-1.836.730.2534.84186662061.0796.7
1.83-1.946.710.4064.34283063031.2798.2
1.94-2.096.930.1498.34403162861.0497.9
2.09-2.36.690.1788.74139861490.8295.5
2.3-2.636.940.0812.94473764220.7199.1
2.63-3.327.020.06317.34572264750.799.6
3.32-31.016.70.04925.44351663780.895.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å31.01 Å
Translation2.5 Å31.01 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.7Ldata scaling
d*TREK9.7Ldata reduction
PHASER1.3.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→31 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2663 / WRfactor Rwork: 0.1993 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7725 / SU B: 5.08 / SU ML: 0.081 / SU R Cruickshank DPI: 0.136 / SU Rfree: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2592 2857 5.1 %RANDOM
Rwork0.1973 ---
obs0.2004 56401 87.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 73.66 Å2 / Biso mean: 27.7234 Å2 / Biso min: 12.88 Å2
Baniso -1Baniso -2Baniso -3
1--1.22 Å20 Å2-1.19 Å2
2--2.11 Å20 Å2
3----1.88 Å2
Refinement stepCycle: LAST / Resolution: 1.54→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3152 0 5 434 3591
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.023314
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.9584568
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6665446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.48724.554112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.16915505
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0811510
X-RAY DIFFRACTIONr_chiral_restr0.0920.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212469
X-RAY DIFFRACTIONr_rigid_bond_restr2.65533314
X-RAY DIFFRACTIONr_sphericity_free28.3115125
X-RAY DIFFRACTIONr_sphericity_bonded10.39153529
LS refinement shellResolution: 1.54→1.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 127 -
Rwork0.31 2057 -
all-2184 -
obs--46.86 %
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)
11.4047-0.84760.13371.09750.27860.96150.12940.08670.1023-0.0433-0.1629-0.0584-0.01920.0630.03350.0527-0.00730.0040.04690.00440.0926-11.347520.5667-8.089
24.4185-1.06221.85030.86571.10124.97750.1759-0.0855-0.1568-0.02660.01170.022-0.0363-0.2113-0.18760.09150.06660.020.09240.02960.0997-49.547929.3668-15.1278
32.87890.5272-0.71891.83780.69013.7068-0.02430.0497-0.03630.04520.3069-0.04960.28630.3587-0.28260.05790.0605-0.02940.1094-0.05330.0697-37.165426.5134-12.4052
43.12270.6018-1.33271.06230.74673.70280.0842-0.2825-0.06620.1160.0506-0.18080.11190.3563-0.13480.10080.0251-0.02780.1539-0.00320.1276-42.038828.9869-4.7193
55.4510.93090.57851.3721-0.18950.67670.10460.6651-0.0635-0.2896-0.1918-0.00940.00710.28360.08720.15610.1315-0.04360.306-0.00490.0404-15.244314.9092-33.5508
61.56880.0529-0.14930.9417-0.12352.6030.22150.2525-0.1476-0.0995-0.20230.07570.2405-0.0073-0.01910.10130.0805-0.04360.1068-0.0480.0534-12.87068.8888-22.6877
71.1841-0.520.13670.4287-0.34980.46710.15660.2322-0.0657-0.0748-0.13830.02710.06940.1058-0.01830.07920.0585-0.02210.1058-0.0610.052-25.995118.2749-26.0821
80.9167-0.2595-0.55110.85621.19612.88640.08080.12630.1156-0.14010.1764-0.0811-0.43240.2173-0.25720.0846-0.01930.0440.0851-0.01310.0556-43.348634.3737-27.6887
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 121
2X-RAY DIFFRACTION2H122 - 144
3X-RAY DIFFRACTION3H145 - 192
4X-RAY DIFFRACTION4H193 - 215
5X-RAY DIFFRACTION5L1 - 24
6X-RAY DIFFRACTION6L25 - 57
7X-RAY DIFFRACTION7L58 - 143
8X-RAY DIFFRACTION8L144 - 213

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