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- PDB-3qq9: Crystal structure of FAB fragment of anti-human RSV (RESPIRATORY ... -

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Basic information

Entry
Database: PDB / ID: 3qq9
TitleCrystal structure of FAB fragment of anti-human RSV (RESPIRATORY SYNCYTIAL VIRUS) F Protein MAB 101F
Components
  • 101F HEAVY CHAIN
  • 101F LIGHT CHAIN
KeywordsIMMUNE SYSTEM / RSV F protein
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsLuo, J. / Tsui, P. / Spurlino, J. / Lewansowski, F. / Heavner, G.A. / Del Vecchio, F.
CitationJournal: To be Published
Title: Crystal Structure of Fab 101F
Authors: Luo, J. / Tsui, P. / Spurlino, J. / Lewansowski, F. / Heavner, G.A. / Del Vecchio, F.
History
DepositionFeb 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence / Category: entity_poly / pdbx_struct_mod_residue
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: 101F LIGHT CHAIN
H: 101F HEAVY CHAIN
C: 101F LIGHT CHAIN
D: 101F HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9249
Polymers96,4444
Non-polymers4805
Water22,2671236
1
L: 101F LIGHT CHAIN
H: 101F HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5105
Polymers48,2222
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-47 kcal/mol
Surface area19300 Å2
MethodPISA
2
C: 101F LIGHT CHAIN
D: 101F HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4144
Polymers48,2222
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-61 kcal/mol
Surface area19200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.306, 84.558, 101.658
Angle α, β, γ (deg.)90.00, 104.87, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-547-

HOH

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Components

#1: Antibody 101F LIGHT CHAIN


Mass: 23895.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens, Mus musculus / Cell line (production host): HEK293 / Production host: homo sapiens (human)
#2: Antibody 101F HEAVY CHAIN


Mass: 24326.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens, Mus musculus / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1236 / 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: 49.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 1M Ammonium Sulphate, 0.2M Lithium Sulfate, Sodium Actate pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 14, 2005
RadiationMonochromator: Accel, double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. all: 96655 / Num. obs: 96655 / % possible obs: 85.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Rmerge(I) obs: 0.034

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6.4_486)refinement
CNXrefinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
CNXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→42.367 Å / SU ML: 0.18 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2171 4846 5.01 %Random
Rwork0.173 ---
obs0.1752 96642 85.1 %-
all-96642 --
Solvent computationShrinkage radii: 0.41 Å / VDW probe radii: 0.6 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.078 Å2 / ksol: 0.514 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.8283 Å2-0 Å2-5.4159 Å2
2---0.5937 Å20 Å2
3---4.422 Å2
Refinement stepCycle: LAST / Resolution: 1.64→42.367 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6583 0 25 1236 7844
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0166861
X-RAY DIFFRACTIONf_angle_d1.5279366
X-RAY DIFFRACTIONf_dihedral_angle_d13.4362466
X-RAY DIFFRACTIONf_chiral_restr0.1121058
X-RAY DIFFRACTIONf_plane_restr0.0081195
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.65780.2562780.21491618X-RAY DIFFRACTION45
1.6578-1.67730.2608840.21011793X-RAY DIFFRACTION50
1.6773-1.69770.2477980.21071980X-RAY DIFFRACTION55
1.6977-1.71920.21591250.19972206X-RAY DIFFRACTION61
1.7192-1.74190.27311370.19732386X-RAY DIFFRACTION67
1.7419-1.76570.28091280.18662620X-RAY DIFFRACTION73
1.7657-1.79090.2141420.19922799X-RAY DIFFRACTION79
1.7909-1.81770.22311540.19173049X-RAY DIFFRACTION84
1.8177-1.84610.25831490.18763203X-RAY DIFFRACTION89
1.8461-1.87630.21221830.18343349X-RAY DIFFRACTION94
1.8763-1.90870.22441910.18293482X-RAY DIFFRACTION97
1.9087-1.94340.20512030.18453492X-RAY DIFFRACTION99
1.9434-1.98080.21241910.17273579X-RAY DIFFRACTION100
1.9808-2.02120.20862110.16593594X-RAY DIFFRACTION100
2.0212-2.06520.19411670.16873593X-RAY DIFFRACTION100
2.0652-2.11320.20291930.16883587X-RAY DIFFRACTION100
2.1132-2.16610.19922050.16523580X-RAY DIFFRACTION100
2.1661-2.22460.24081830.16413584X-RAY DIFFRACTION100
2.2246-2.29010.20262010.16593544X-RAY DIFFRACTION99
2.2901-2.3640.22772410.15873570X-RAY DIFFRACTION100
2.364-2.44850.19011800.16443570X-RAY DIFFRACTION100
2.4485-2.54650.21391810.16113590X-RAY DIFFRACTION100
2.5465-2.66240.22371760.16573602X-RAY DIFFRACTION100
2.6624-2.80270.19171850.15763581X-RAY DIFFRACTION99
2.8027-2.97830.21271940.15283573X-RAY DIFFRACTION99
2.9783-3.20810.19651830.15473518X-RAY DIFFRACTION97
3.2081-3.53080.21570.15993257X-RAY DIFFRACTION90
3.5308-4.04140.221280.1692723X-RAY DIFFRACTION75
4.0414-5.09040.1903980.19181977X-RAY DIFFRACTION54
5.0904-42.38140.39361000.30011797X-RAY DIFFRACTION49
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)
10.32340.35510.06851.5030.34710.9919-0.0735-0.0070.00830.02470.14030.180.0090.0348-0.07710.080.02570.03560.10320.04220.18943.66890.590756.21
21.2949-0.05420.78371.33520.63541.09480.14290.2987-0.2519-0.47520.09050.12250.15330.1634-0.20410.2896-0.0271-0.0720.2355-0.01770.1917-1.729711.373720.1179
30.89790.1225-0.23470.5541-0.22090.8173-0.0591-0.11150.07080.02820.0808-0.02070.01530.0574-0.03270.13340.01140.02310.14780.00080.19512.389121.0758.0172
40.7581-0.01660.51020.62810.21340.76030.01430.028-0.1839-0.0240.03230.02860.0398-0.1327-0.04280.1623-0.04190.01240.2090.02640.1845-3.529824.024530.1111
50.7850.18650.99670.9644-0.12391.8993-0.18080.17870.20240.1967-0.205-0.0829-0.20630.50950.31790.2744-0.0318-0.07440.29390.1010.268318.082613.17591.011
61.06760.49011.09521.3240.82621.6169-0.1602-0.28470.2163-0.1052-0.17770.0195-0.2621-0.29520.28960.25340.0797-0.04940.2814-0.09930.237418.17675.1839127.2745
70.49030.11620.15261.2214-0.86081.0340.08520.0085-0.0479-0.1322-0.0781-0.00120.19830.0158-0.02460.30430.0453-0.02290.2040.00160.16631.2033-1.80290.547
80.77430.42330.43750.4390.31032.1858-0.2134-0.7910.4467-0.2126-0.26350.4625-0.1991-0.99490.4620.19780.2165-0.11990.5638-0.30370.32042.46327.7252122.7977
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain L and resseq 1:112 and not element H
2X-RAY DIFFRACTION2chain L and resseq 113:217 and not element H
3X-RAY DIFFRACTION3chain H and resseq 1:120 and not element H
4X-RAY DIFFRACTION4chain H and resseq 121:220 and not element H
5X-RAY DIFFRACTION5chain C and resseq 1:112 and not element H
6X-RAY DIFFRACTION6chain C and resseq 113:217 and not element H
7X-RAY DIFFRACTION7chain D and resseq 1:120 and not element H
8X-RAY DIFFRACTION8chain D and resseq 121:220 and not element H

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