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- PDB-4llv: The structure of the unbound form of anti-HIV antibody 4E10 Fv -

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Basic information

Entry
Database: PDB / ID: 4llv
TitleThe structure of the unbound form of anti-HIV antibody 4E10 Fv
Components
  • 4E10 Fv heavy chain
  • 4E10 Fv light chain
KeywordsIMMUNE SYSTEM / 4E10 / FV / HIV / immunoglobulin / Antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsFinton, K.A.K. / Rupert, P.B. / Strong, R.K.
CitationJournal: Plos Pathog. / Year: 2013
Title: Autoreactivity and Exceptional CDR Plasticity (but Not Unusual Polyspecificity) Hinder Elicitation of the Anti-HIV Antibody 4E10.
Authors: Finton, K.A. / Larimore, K. / Larman, H.B. / Friend, D. / Correnti, C. / Rupert, P.B. / Elledge, S.J. / Greenberg, P.D. / Strong, R.K.
History
DepositionJul 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4E10 Fv heavy chain
B: 4E10 Fv light chain
C: 4E10 Fv heavy chain
D: 4E10 Fv light chain
E: 4E10 Fv heavy chain
F: 4E10 Fv light chain
H: 4E10 Fv heavy chain
L: 4E10 Fv light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,85323
Polymers103,4358
Non-polymers1,41715
Water5,242291
1
A: 4E10 Fv heavy chain
B: 4E10 Fv light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4238
Polymers25,8592
Non-polymers5646
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-42 kcal/mol
Surface area11080 Å2
MethodPISA
2
E: 4E10 Fv heavy chain
F: 4E10 Fv light chain


Theoretical massNumber of molelcules
Total (without water)25,8592
Polymers25,8592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-22 kcal/mol
Surface area10380 Å2
MethodPISA
3
H: 4E10 Fv heavy chain
L: 4E10 Fv light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3317
Polymers25,8592
Non-polymers4725
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-31 kcal/mol
Surface area10590 Å2
MethodPISA
4
C: 4E10 Fv heavy chain
D: 4E10 Fv light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2396
Polymers25,8592
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.917, 161.518, 163.274
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11L-317-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13A
23H
14B
24F
15B
25L
16C
26E
17C
27H
18E
28H
19F
29L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 127
2010C1 - 127
1020A1 - 126
2020E1 - 126
1030A2 - 125
2030H2 - 125
1040B129 - 231
2040F129 - 231
1050B128 - 234
2050L128 - 234
1060C1 - 126
2060E1 - 126
1070C2 - 125
2070H2 - 125
1080E2 - 126
2080H2 - 126
1090F129 - 231
2090L129 - 231

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9

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Components

#1: Antibody
4E10 Fv heavy chain


Mass: 13756.434 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293 / Production host: Homo sapiens (human)
#2: Antibody
4E10 Fv light chain


Mass: 12102.424 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): HEK 293 / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.83 Å3/Da / Density % sol: 56.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M NaOAc, 0.8M Li2SO4, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 13, 2013
RadiationMonochromator: Double-crystal, Si(111) liquid N2 cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. all: 46684 / Num. obs: 46684 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.39→2.44 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→46.1 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.894 / SU B: 12.389 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.335 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24516 2353 5.1 %RANDOM
Rwork0.21551 ---
obs0.21702 44146 99.19 %-
all-46684 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.663 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20 Å2
2--0.85 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.39→46.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6427 0 81 291 6799
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.026679
X-RAY DIFFRACTIONr_bond_other_d0.0020.025943
X-RAY DIFFRACTIONr_angle_refined_deg0.8991.9549128
X-RAY DIFFRACTIONr_angle_other_deg0.7173.00313567
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9365892
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.26322.751229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27515876
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0241537
X-RAY DIFFRACTIONr_chiral_restr0.0610.21040
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0217706
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021552
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: INTERATOMIC DISTANCE / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A63490.13
12C63490.13
21A47840.16
22E47840.16
31A54900.19
32H54900.19
41B40830.11
42F40830.11
51B50420.14
52L50420.14
61C47750.17
62E47750.17
71C54890.19
72H54890.19
81E50180.14
82H50180.14
91F40740.13
92L40740.13
LS refinement shellResolution: 2.39→2.452 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 155 -
Rwork0.265 2976 -
obs--91.9 %
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)
13.91040.518-1.44242.01460.19974.68360.0258-0.06340.0237-0.14980.0627-0.0533-0.12080.2533-0.08850.1789-0.02520.01830.1048-0.01610.1045-65.7988-35.36934.3802
25.63360.3713-2.20464.7806-0.26574.94430.40020.48441.184-0.41520.09040.5294-0.4441-0.7203-0.49070.41180.10940.04840.21110.1250.507-78.7968-18.3572-0.8421
31.58090.2488-0.54950.99440.49049.28610.087-0.10730.09760.0407-0.1330.0947-0.3224-0.67190.04590.28360.021-0.03950.3516-0.02870.1237-57.1915-36.9321-39.3145
412.60780.3699-6.02023.40240.48276.28770.35430.24820.58110.0549-0.21120.9258-0.7324-1.4569-0.14320.54590.3252-0.06081.0843-0.10690.4588-75.6875-30.4937-39.409
53.28210.67240.89966.7566-1.21111.3156-0.1738-0.0972-0.8842-0.04160.0111-0.07060.1264-0.43720.16280.3907-0.16860.12150.5953-0.13540.5565-60.7183-60.4703-16.4529
65.64740.12544.50452.3886-1.1165.9503-0.73190.334-0.6005-0.60350.67130.5243-0.1896-1.31010.06060.7824-0.33640.03031.2062-0.31850.7598-76.229-60.5131-30.9302
75.3593-0.15550.68282.40911.26292.1526-0.01340.23490.408-0.13090.09590.03-0.12740.0473-0.08250.2360.00490.01290.1065-0.00950.137-37.5927-29.71-13.2323
84.52450.4147-0.05064.71220.72393.0569-0.12750.01390.56370.0070.0876-0.1069-0.0628-0.02720.03990.14790.0132-0.01910.0114-0.05440.4134-44.7933-11.9012-2.5637
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 113
2X-RAY DIFFRACTION2B1 - 110
3X-RAY DIFFRACTION3C1 - 113
4X-RAY DIFFRACTION4D2 - 104
5X-RAY DIFFRACTION5E1 - 112
6X-RAY DIFFRACTION6F2 - 104
7X-RAY DIFFRACTION7H2 - 112
8X-RAY DIFFRACTION8L1 - 107

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