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- PDB-6l8t: Crystal structure of the Fab fragment of a humanized HBV therapeu... -

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Basic information

Entry
Database: PDB / ID: 6l8t
TitleCrystal structure of the Fab fragment of a humanized HBV therapeutic antibody
Components
  • Antibody heavy chainImmunoglobulin heavy chain
  • Antibody light chainImmunoglobulin light chain
KeywordsIMMUNE SYSTEM / Antibody
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.766 Å
AuthorsHe, M.Z. / Gu, Y. / Li, S.W.
CitationJournal: Antiviral Res. / Year: 2020
Title: Structure guided maturation of a novel humanized anti-HBV antibody and its preclinical development.
Authors: Zhou, B. / Xia, L. / Zhang, T. / You, M. / Huang, Y. / He, M. / Su, R. / Tang, J. / Zhang, J. / Li, S. / An, Z. / Yuan, Q. / Luo, W. / Xia, N.
History
DepositionNov 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: 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: Antibody light chain
H: Antibody heavy chain
B: Antibody light chain
A: Antibody heavy chain
D: Antibody light chain
C: Antibody heavy chain


Theoretical massNumber of molelcules
Total (without water)143,1796
Polymers143,1796
Non-polymers00
Water27,8691547
1
L: Antibody light chain
H: Antibody heavy chain


Theoretical massNumber of molelcules
Total (without water)47,7262
Polymers47,7262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-25 kcal/mol
Surface area20740 Å2
MethodPISA
2
B: Antibody light chain
A: Antibody heavy chain


Theoretical massNumber of molelcules
Total (without water)47,7262
Polymers47,7262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-26 kcal/mol
Surface area20430 Å2
MethodPISA
3
D: Antibody light chain
C: Antibody heavy chain


Theoretical massNumber of molelcules
Total (without water)47,7262
Polymers47,7262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-26 kcal/mol
Surface area20290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.942, 75.943, 137.550
Angle α, β, γ (deg.)90.000, 103.240, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Antibody light chain / Immunoglobulin light chain


Mass: 24082.857 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Antibody heavy chain / Immunoglobulin heavy chain


Mass: 23643.369 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1547 / 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: 2.77 Å3/Da / Density % sol: 55.56 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.2 M ammonium acetate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 152195 / % possible obs: 99.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.034 / Rrim(I) all: 0.067 / Χ2: 1.087 / Net I/σ(I): 11.4 / Num. measured all: 568776
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.76-1.793.70.65375190.6840.3970.7660.96999.9
1.79-1.823.70.52775830.7940.3190.6180.992100
1.82-1.863.70.42776280.8420.2580.50.994100
1.86-1.93.70.33976410.8940.2050.3971.013100
1.9-1.943.70.27276270.9290.1640.3181.029100
1.94-1.983.70.22475460.9460.1360.2631.058100
1.98-2.033.70.18176150.9640.1090.2121.081100
2.03-2.093.80.15176150.9770.0910.1761.132100
2.09-2.153.80.12675740.9820.0750.1471.12299.8
2.15-2.223.80.10876280.9870.0650.1271.14199.9
2.22-2.33.80.10176300.9880.0610.1181.18799.7
2.3-2.393.80.09176020.990.0540.1061.18899.9
2.39-2.53.80.08576220.9910.050.0991.16299.6
2.5-2.633.80.08375790.9910.050.0971.25799.9
2.63-2.793.80.07576430.9910.0450.0871.24299.6
2.79-3.013.70.07176230.9910.0420.0831.10399.7
3.01-3.313.70.05976300.9940.0350.0681.03399.7
3.31-3.793.60.03976140.9970.0230.0451.02399.3
3.79-4.783.80.0377060.9980.0180.0350.96399.7
4.78-103.70.03375700.9970.020.0391.04196.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
HKL-2000data reduction
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MAU
Resolution: 1.766→26.537 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.31
RfactorNum. reflection% reflection
Rfree0.1923 7493 4.92 %
Rwork0.1649 --
obs0.1663 152165 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 152.97 Å2 / Biso mean: 41.5239 Å2 / Biso min: 10.62 Å2
Refinement stepCycle: final / Resolution: 1.766→26.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10076 0 0 1547 11623
Biso mean---44.11 -
Num. residues----1317
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510340
X-RAY DIFFRACTIONf_angle_d1.00814059
X-RAY DIFFRACTIONf_chiral_restr0.0361593
X-RAY DIFFRACTIONf_plane_restr0.0041787
X-RAY DIFFRACTIONf_dihedral_angle_d13.343692
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.766-1.78590.2792090.2619426488
1.7859-1.80690.28732650.24964789100
1.8069-1.82890.27242440.23234806100
1.8289-1.85210.26122450.22524898100
1.8521-1.87640.24142480.21154793100
1.8764-1.90210.23862580.20594900100
1.9021-1.92930.24342250.1954768100
1.9293-1.95810.24312810.19324838100
1.9581-1.98870.22222500.18864876100
1.9887-2.02130.22612420.18324787100
2.0213-2.05610.21272770.17724900100
2.0561-2.09350.20232580.17594808100
2.0935-2.13370.22242260.17654826100
2.1337-2.17730.20042440.17094880100
2.1773-2.22460.23122370.16994856100
2.2246-2.27630.19122270.16944830100
2.2763-2.33320.21722340.16864854100
2.3332-2.39620.20642380.17234837100
2.3962-2.46670.18712390.17034855100
2.4667-2.54630.20512610.1744832100
2.5463-2.63720.222540.17564821100
2.6372-2.74270.20512770.17364824100
2.7427-2.86740.2022860.17284826100
2.8674-3.01830.19412480.16664861100
3.0183-3.20710.19382710.16844864100
3.2071-3.45430.17842310.16024867100
3.4543-3.8010.17022580.1499483799
3.801-4.34890.16062570.14034897100
4.3489-5.47130.13852470.12484913100
5.4713-100.1842560.1633476595
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)
12.79491.8008-0.87196.612-3.16014.529-0.1747-0.51070.01690.51010.26960.5573-0.42750.0121-0.17220.55580.08370.17440.45710.09180.2752-34.6743-14.00561.3303
22.1990.7455-0.12634.9622-2.32723.9642-0.0363-0.32550.08410.5589-0.0576-0.1373-0.53770.55520.15710.5746-0.0660.06610.50270.07430.2196-25.2819-13.5713-1.2927
30.45870.8218-0.8544.0956-2.85021.86690.1384-0.441-0.01260.9742-0.03890.4276-0.48410.1326-0.14420.4761-0.00850.14280.38860.10180.3155-33.3114-9.4437-7.905
44.85041.72783.14422.93151.43263.0570.1137-0.04330.450.1615-0.06850.59550.0587-0.0894-0.04560.24230.01540.08480.18670.07120.3275-42.38411.4095-31.2204
55.82891.92794.25912.34131.48314.74340.04180.07440.68210.1453-0.13010.5159-0.1719-0.15630.12530.2419-0.00090.12290.23530.08480.3331-41.96074.5056-30.6666
64.6382-1.34195.69225.8778-1.56947.46450.0154-0.05570.1394-0.24790.01860.36190.27860.29390.02120.2955-0.02950.05250.37860.06080.2134-28.3907-30.8136-22.0079
71.82740.3078-1.65852.98850.87841.9379-0.2553-0.5478-0.50950.42060.33320.17810.18960.4308-0.08450.36460.03770.03370.43850.14440.2604-25.7643-32.9566-11.4681
82.74310.8258-0.25716.6422-2.8045.40810.0038-0.3207-0.37550.28070.32191.04690.1102-0.0201-0.32410.33130.01190.08080.37080.16010.3029-33.633-31.778-8.704
94.1479-1.25781.46193.9656-1.08832.8952-0.0618-0.145-0.93420.09530.21560.77150.4574-0.0922-0.09060.3909-0.00270.03720.31410.19590.4271-32.1985-38.0099-14.3413
108.65821.63174.65556.5861-0.09742.9156-0.42080.02230.3155-0.33070.36460.64690.0383-0.1372-0.0030.3067-0.02660.05240.35720.16250.2737-35.118-27.4365-19.1652
111.2696-1.85832.26662.9068-3.87626.64750.1453-0.1461-0.2771-0.12990.1280.30660.2528-0.0213-0.12080.3083-0.05420.01510.30330.08960.2567-30.3001-24.0052-22.8623
125.11080.97892.5610.39860.13675.1452-0.16480.01620.8935-0.2574-0.15940.6233-0.8096-0.10470.24210.35330.01590.02560.29270.10070.3547-33.81987.0722-40.0385
131.56550.90660.38972.5174-0.16331.55510.1448-0.0482-0.06390.1536-0.0080.20490.1532-0.0962-0.15690.22440.01390.00120.20870.07030.1974-30.1987-5.0139-34.5393
143.64481.508-0.62172.6399-3.69135.53430.0570.0536-0.3251-0.2846-0.1466-0.3790.24040.25490.22940.1350.055-0.00910.22320.03250.1857-24.5805-4.0682-41.5685
153.043-2.59263.59633.6922-5.02266.4477-0.03790.03440.0904-0.26960.21110.05440.0672-0.2425-0.11650.1794-0.01260.00710.27150.0720.2522-32.60311.6701-48.3979
162.77850.5922-0.25551.8699-0.04471.65210.01250.1426-0.0749-0.03870.0423-0.23890.10310.1757-0.04870.10490.0255-0.01830.167-0.05590.18465.2391-20.7695-68.8971
172.26442.02871.45242.51291.44261.049-0.00030.1554-0.0920.13240.1772-0.29410.07470.1676-0.16120.11320.0148-0.02060.1598-0.03090.21693.969-15.1825-60.8624
188.3756-3.8175-3.0163.22712.09533.84850.119-0.33350.37180.1323-0.0064-0.1971-0.0872-0.0749-0.10190.1472-0.0394-0.04580.1689-0.05850.21360.0277.0869-44.2901
195.9809-1.8326-2.0221.76971.14573.6397-0.1181-0.79120.20750.3150.1838-0.2098-0.13490.1501-0.07460.2052-0.0164-0.03330.1945-0.02590.22571.04065.1242-41.2987
208.0134-3.2008-5.60916.17864.02315.18220.37920.33520.4245-0.4745-0.1617-0.0384-0.7658-0.1217-0.45390.09940.0025-0.08920.19960.00720.182-18.9715-7.9247-70.8347
213.44080.31381.00462.78571.01713.5442-0.01620.2833-0.0427-0.1019-0.00610.11380.03370.0049-0.00290.0857-0.00910.0060.133-0.01950.1294-17.7003-18.679-73.7088
228.7743-0.6636-4.68544.28083.73067.05620.0142-0.23080.12370.0574-0.02150.17730.09390.1672-0.02750.08580.021-0.02670.06850.01930.1252-16.7857-12.2873-64.405
230.28770.0915-0.39761.59370.86811.13590.03440.03040.11240.11170.0806-0.0587-0.01020.1127-0.0980.11680.0064-0.01170.1537-0.00490.2053-7.77153.1208-58.6961
243.8821.832-0.06361.32630.03710.82790.03310.05760.0914-0.0268-0.0337-0.0437-0.04620.0420.01340.1090.01860.01090.10160.00330.2082-3.332610.534-55.9187
253.08583.43463.01267.49452.25842.9712-0.20270.25170.1176-0.29520.1749-0.3173-0.2424-0.02410.18310.1340.01430.0350.15720.03370.2287-5.836117.2999-60.7001
260.5558-0.6065-1.17373.62481.93672.48910.1104-0.14510.24470.44520.1803-0.3351-0.3010.0477-0.40020.34330.0283-0.01180.2044-0.00780.5292-5.445323.8711-49.7256
273.6009-0.99721.34123.6971-0.74528.79330.0291-0.4668-0.04910.17040.17160.258-0.6864-0.4204-0.1530.1910.06550.04080.40280.0420.2468-10.6956-29.8109-21.2765
288.04-1.83355.96775.5444-4.93038.74650.11060.6514-0.2469-0.8134-0.26710.52910.0505-0.86980.06120.1598-0.04860.00520.44940.10040.2857-15.3232-37.0706-35.783
295.75255.78610.21177.76192.66253.13380.1142-0.4564-0.52750.2613-0.0286-0.4210.09620.171-0.15090.25860.0303-0.03620.2620.0730.227-1.0828-35.9067-26.8949
303.02051.2711-0.46643.31292.20815.874-0.0565-0.4384-0.39160.3025-0.01940.13420.4777-0.3341-0.02890.21840.03190.00640.36380.1460.2856-8.1338-39.9019-23.4584
311.0850.46140.29232.281.69963.7990.0611-0.3995-0.03080.1677-0.16010.2362-0.1427-0.50690.06540.27970.070.00430.41560.07290.2305-6.3543-27.698-23.2849
327.39132.7413-1.16648.8728-1.29218.49790.5937-0.36490.93380.22070.2576-0.6046-1.44780.339-0.67370.7506-0.00880.15410.4207-0.20840.470715.2807-0.4356-12.7842
334.90653.694-1.71813.3435-2.22923.60320.3924-0.05630.70240.0214-0.02320.5757-0.8597-1.011-0.32170.67740.17420.12020.6412-0.04470.39491.049-8.5734-12.0358
342.70961.8985-0.74238.2811-0.50843.51970.215-0.19290.71920.33130.03170.4145-1.1113-0.8319-0.19670.7270.23010.06620.5979-0.03260.43793.7771-3.4436-12.2703
353.69580.42020.97066.64170.98094.72830.0348-0.1096-0.39080.53080.1189-0.26030.17150.1683-0.11130.2293-0.0035-0.00410.23840.01820.149911.9105-34.5001-40.9126
362.1756-0.2235-0.18452.580.54633.54780.0099-0.0459-0.073-0.08790.0180.0746-0.30930.0026-0.02460.2616-0.0058-0.0430.10550.01480.17374.8261-32.0351-44.722
371.34720.71270.86461.80560.49261.0557-0.0591-0.24520.1521-0.04750.03770.1235-0.3849-0.00950.03530.4143-0.01010.01670.2546-0.03330.221511.1452-19.0406-27.9746
381.55690.53360.45121.3283-1.32575.94180.0342-0.3080.10450.07130.017-0.12010.19980.0338-0.08650.517-0.0199-0.0280.3266-0.0910.257517.7826-13.9695-14.7032
391.372.79110.31395.49080.66240.04070.3168-0.153-0.06540.5933-0.66880.06240.3135-0.54160.36270.56-0.0665-0.06660.5981-0.15590.374425.1597-3.3872-8.8622
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 37 )L1 - 37
2X-RAY DIFFRACTION2chain 'L' and (resid 38 through 95 )L38 - 95
3X-RAY DIFFRACTION3chain 'L' and (resid 96 through 118 )L96 - 118
4X-RAY DIFFRACTION4chain 'L' and (resid 119 through 168 )L119 - 168
5X-RAY DIFFRACTION5chain 'L' and (resid 169 through 219 )L169 - 219
6X-RAY DIFFRACTION6chain 'H' and (resid 1 through 17 )H1 - 17
7X-RAY DIFFRACTION7chain 'H' and (resid 18 through 41 )H18 - 41
8X-RAY DIFFRACTION8chain 'H' and (resid 42 through 60 )H42 - 60
9X-RAY DIFFRACTION9chain 'H' and (resid 61 through 83 )H61 - 83
10X-RAY DIFFRACTION10chain 'H' and (resid 84 through 98 )H84 - 98
11X-RAY DIFFRACTION11chain 'H' and (resid 99 through 119 )H99 - 119
12X-RAY DIFFRACTION12chain 'H' and (resid 120 through 134 )H120 - 134
13X-RAY DIFFRACTION13chain 'H' and (resid 135 through 188 )H135 - 188
14X-RAY DIFFRACTION14chain 'H' and (resid 189 through 203 )H189 - 203
15X-RAY DIFFRACTION15chain 'H' and (resid 204 through 220 )H204 - 220
16X-RAY DIFFRACTION16chain 'B' and (resid 1 through 95 )B1 - 95
17X-RAY DIFFRACTION17chain 'B' and (resid 96 through 118 )B96 - 118
18X-RAY DIFFRACTION18chain 'B' and (resid 119 through 155 )B119 - 155
19X-RAY DIFFRACTION19chain 'B' and (resid 156 through 219 )B156 - 219
20X-RAY DIFFRACTION20chain 'A' and (resid 1 through 17 )A1 - 17
21X-RAY DIFFRACTION21chain 'A' and (resid 18 through 83 )A18 - 83
22X-RAY DIFFRACTION22chain 'A' and (resid 84 through 98 )A84 - 98
23X-RAY DIFFRACTION23chain 'A' and (resid 99 through 134 )A99 - 134
24X-RAY DIFFRACTION24chain 'A' and (resid 135 through 190 )A135 - 190
25X-RAY DIFFRACTION25chain 'A' and (resid 191 through 203 )A191 - 203
26X-RAY DIFFRACTION26chain 'A' and (resid 204 through 220 )A204 - 220
27X-RAY DIFFRACTION27chain 'D' and (resid 1 through 18 )D1 - 18
28X-RAY DIFFRACTION28chain 'D' and (resid 19 through 37 )D19 - 37
29X-RAY DIFFRACTION29chain 'D' and (resid 38 through 53 )D38 - 53
30X-RAY DIFFRACTION30chain 'D' and (resid 54 through 95 )D54 - 95
31X-RAY DIFFRACTION31chain 'D' and (resid 96 through 118 )D96 - 118
32X-RAY DIFFRACTION32chain 'D' and (resid 119 through 134 )D119 - 134
33X-RAY DIFFRACTION33chain 'D' and (resid 135 through 155 )D135 - 155
34X-RAY DIFFRACTION34chain 'D' and (resid 156 through 219 )D156 - 219
35X-RAY DIFFRACTION35chain 'C' and (resid 1 through 34 )C1 - 34
36X-RAY DIFFRACTION36chain 'C' and (resid 35 through 83 )C35 - 83
37X-RAY DIFFRACTION37chain 'C' and (resid 84 through 134 )C84 - 134
38X-RAY DIFFRACTION38chain 'C' and (resid 135 through 203 )C135 - 203
39X-RAY DIFFRACTION39chain 'C' and (resid 204 through 220 )C204 - 220

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