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- PDB-3v6f: Crystal Structure of an anti-HBV e-antigen monoclonal Fab fragmen... -

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Basic information

Entry
Database: PDB / ID: 3v6f
TitleCrystal Structure of an anti-HBV e-antigen monoclonal Fab fragment (e6), unbound
Components
  • Fab e6 Heavy Chain
  • Fab e6 Light Chain
KeywordsIMMUNE SYSTEM / immunoglobulin domain / antibody Fab fragment
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsDimattia, M.A. / Watts, N.R. / Stahl, S.J. / Grimes, J.M. / Steven, A.C. / Stuart, D.I. / Wingfield, P.T.
CitationJournal: Structure / Year: 2013
Title: Antigenic switching of hepatitis B virus by alternative dimerization of the capsid protein.
Authors: Dimattia, M.A. / Watts, N.R. / Stahl, S.J. / Grimes, J.M. / Steven, A.C. / Stuart, D.I. / Wingfield, P.T.
History
DepositionDec 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 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: Fab e6 Heavy Chain
B: Fab e6 Light Chain
C: Fab e6 Heavy Chain
D: Fab e6 Light Chain
E: Fab e6 Heavy Chain
F: Fab e6 Light Chain
H: Fab e6 Heavy Chain
L: Fab e6 Light Chain


Theoretical massNumber of molelcules
Total (without water)192,3818
Polymers192,3818
Non-polymers00
Water8,449469
1
A: Fab e6 Heavy Chain
B: Fab e6 Light Chain


Theoretical massNumber of molelcules
Total (without water)48,0952
Polymers48,0952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-24 kcal/mol
Surface area19370 Å2
MethodPISA
2
C: Fab e6 Heavy Chain
D: Fab e6 Light Chain


Theoretical massNumber of molelcules
Total (without water)48,0952
Polymers48,0952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-24 kcal/mol
Surface area19410 Å2
MethodPISA
3
E: Fab e6 Heavy Chain
F: Fab e6 Light Chain


Theoretical massNumber of molelcules
Total (without water)48,0952
Polymers48,0952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-24 kcal/mol
Surface area19240 Å2
MethodPISA
4
H: Fab e6 Heavy Chain
L: Fab e6 Light Chain


Theoretical massNumber of molelcules
Total (without water)48,0952
Polymers48,0952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-25 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.120, 68.240, 236.640
Angle α, β, γ (deg.)90.00, 96.27, 90.00
Int Tables number5
Space group name H-MC121
DetailsChain H and L form one copy of the biological assembly (Fab fragment).

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Components

#1: Antibody
Fab e6 Heavy Chain


Mass: 23765.408 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody
Fab e6 Light Chain


Mass: 24329.928 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 469 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.49 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.52→31.1 Å / Num. obs: 66469 / % possible obs: 99.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 58.39 Å2

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Processing

SoftwareName: BUSTER / Version: 2.11.2 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.52→31.06 Å / Cor.coef. Fo:Fc: 0.9375 / Cor.coef. Fo:Fc free: 0.9151 / SU R Cruickshank DPI: 0.491 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2197 3376 5.08 %RANDOM
Rwork0.1789 ---
obs0.181 66468 99.33 %-
Displacement parametersBiso mean: 62.32 Å2
Baniso -1Baniso -2Baniso -3
1--11.5158 Å20 Å23.3087 Å2
2---0.8106 Å20 Å2
3---12.3265 Å2
Refine analyzeLuzzati coordinate error obs: 0.359 Å
Refinement stepCycle: LAST / Resolution: 2.52→31.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13262 0 0 469 13731
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113597HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2718511HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4455SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes264HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1970HARMONIC5
X-RAY DIFFRACTIONt_it13597HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.43
X-RAY DIFFRACTIONt_other_torsion21.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1832SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14708SEMIHARMONIC4
LS refinement shellResolution: 2.52→2.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2756 251 5.32 %
Rwork0.2363 4468 -
all0.2385 4719 -
obs--99.33 %
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)
12.09890.3857-0.33660.9808-0.79674.43730.20810.15880.1410.36680.03160.2329-0.4999-0.2591-0.23980.03510.06680.1281-0.09120.0481-0.133922.3846-40.957280.8011
24.396-0.3853-0.04624.1999-2.96948.0037-0.0531-0.57930.51880.03040.129-0.0228-0.53960.2892-0.0758-0.133-0.08250.0836-0.0179-0.162-0.125841.715-32.22554.7699
31.59980.06130.10751.4575-0.09472.58020.02380.09980.1509-0.1654-0.0667-0.0376-0.16970.07060.0429-0.04550.05880.005-0.0732-0.0115-0.030328.7341-24.2848-14.8369
44.24941.28051.43271.70041.6054.60540.0324-0.19160.0027-0.0613-0.16680.2416-0.323-0.340.1343-0.1625-0.0140.021-0.0504-0.02720.04526.6949-21.814110.9959
51.68090.0028-0.55323.3771-0.57753.7062-0.00520.07060.04010.15810.10670.15410.1383-0.039-0.10140.0122-0.02860.0856-0.1134-0.0038-0.142813.6833-19.1823132.0091
62.6706-1.2070.02952.39821.11294.53720.09150.1558-0.4957-0.0788-0.08620.5389-0.023-0.3218-0.0053-0.1486-0.0959-0.1095-0.10150.03280.0955-4.165-21.3871103.1169
70.36510.5975-0.04992.86440.49712.4560.0574-0.1502-0.0530.0955-0.0178-0.1411-0.02760.0523-0.0396-0.1253-0.04610.00950.05720.0039-0.06127.8328-2.844736.8445
85.73031.5209-1.17454.0878-2.76084.638-0.30030.032-0.55970.40410.16650.17250.49390.52530.13380.24990.15290.0541-0.2771-0.0879-0.2638.8719-12.03667.1426
92.7040.007-0.12992.16060.92815.67480.05680.218-0.1029-0.1272-0.0656-0.313-0.03830.52820.0088-0.16460.01190.0207-0.05330.0049-0.030443.103-22.40591.3787
105.14381.19151.49312.96830.31643.2384-0.0329-0.398-0.54860.04480.02640.39210.3848-0.56160.0064-0.1405-0.03620.0692-0.09430.0884-0.017712.0989-31.514723.2184
113.6335-1.21160.51723.4498-2.38387.1130.1792-0.0427-0.12750.04780.250.5478-0.1008-0.5522-0.4291-0.31660.04460.04830.1260.1578-0.147.2186-42.625165.3207
127.9458-1.09142.00671.75120.26682.40370.1103-0.2312-0.5123-0.18090.1514-0.1581-0.19420.2391-0.2616-0.051-0.08720.0596-0.09610.0283-0.09338.7994-42.383442.3668
132.8516-0.2485-1.08123.1130.98327.4909-0.0014-0.3330.1821-0.01440.1549-0.4602-0.0180.5104-0.1535-0.0907-0.07690.0997-0.1214-0.1034-0.140430.378-20.9246118.1967
147.8678-2.20570.65583.48420.29842.85-0.00950.0160.2557-0.60010.13260.4785-0.3046-0.5046-0.12310.0989-0.023-0.1258-0.18730.1504-0.16952.8777-11.853392.1664
154.08430.8469-1.63663.7321-0.22966.10820.2191-0.03810.40540.1628-0.24460.5351-0.1612-0.27340.0255-0.2613-0.00820.08650.004-0.0105-0.0998.9187-0.947647.5506
166.68730.74721.42493.27011.06756.6416-0.16510.06770.12490.51510.2285-0.22210.54110.5534-0.06330.16030.1434-0.0468-0.26840.0101-0.311332.8051-2.076178.3016
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|1 - 118}A1 - 118
2X-RAY DIFFRACTION2{A|119 - 219}A119 - 219
3X-RAY DIFFRACTION3{H|1 - 118}H1 - 118
4X-RAY DIFFRACTION4{H|119 - 219}H119 - 219
5X-RAY DIFFRACTION5{C|1 - 118}C1 - 118
6X-RAY DIFFRACTION6{C|119 - 219}C119 - 219
7X-RAY DIFFRACTION7{E|1 - 118}E1 - 118
8X-RAY DIFFRACTION8{E|119 - 219}E119 - 219
9X-RAY DIFFRACTION9{L|1 - 115}L1 - 115
10X-RAY DIFFRACTION10{L|116 - 219}L116 - 219
11X-RAY DIFFRACTION11{B|1 - 115}B1 - 115
12X-RAY DIFFRACTION12{B|116 - 219}B116 - 219
13X-RAY DIFFRACTION13{D|1 - 115}D1 - 115
14X-RAY DIFFRACTION14{D|116 - 219}D116 - 219
15X-RAY DIFFRACTION15{F|1 - 115}F1 - 115
16X-RAY DIFFRACTION16{F|116 - 219}F116 - 219

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