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- PDB-6wj0: Crystal structure of Fab 54-4H03 -

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Basic information

Entry
Database: PDB / ID: 6wj0
TitleCrystal structure of Fab 54-4H03
Components
  • Fab 54-4H03 heavy chain
  • Fab 54-4H03 light chain
KeywordsIMMUNE SYSTEM / Antibody
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.802 Å
AuthorsWu, N.C. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56 AI127371 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)K99 AI139445 United States
CitationJournal: Cell Host Microbe / Year: 2020
Title: Convergent Evolution in Breadth of Two VH6-1-Encoded Influenza Antibody Clonotypes from a Single Donor.
Authors: Wu, N.C. / Andrews, S.F. / Raab, J.E. / O'Connell, S. / Schramm, C.A. / Ding, X. / Chambers, M.J. / Leung, K. / Wang, L. / Zhang, Y. / Mascola, J.R. / Douek, D.C. / Ledgerwood, J.E. / ...Authors: Wu, N.C. / Andrews, S.F. / Raab, J.E. / O'Connell, S. / Schramm, C.A. / Ding, X. / Chambers, M.J. / Leung, K. / Wang, L. / Zhang, Y. / Mascola, J.R. / Douek, D.C. / Ledgerwood, J.E. / McDermott, A.B. / Wilson, I.A.
History
DepositionApr 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Sep 23, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 18, 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
H: Fab 54-4H03 heavy chain
L: Fab 54-4H03 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6644
Polymers48,4802
Non-polymers1842
Water8,215456
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-26 kcal/mol
Surface area20110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.441, 80.069, 107.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11H-600-

HOH

21H-612-

HOH

31L-405-

HOH

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Components

#1: Antibody Fab 54-4H03 heavy chain


Mass: 24881.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab 54-4H03 light chain


Mass: 23598.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 456 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.68 Å3/Da / Density % sol: 54.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 8000, 0.2 M NaCl, and 0.1 M phosphate-citrate pH 4.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 48821 / % possible obs: 100 % / Redundancy: 7.6 % / Biso Wilson estimate: 28.19 Å2 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.023 / Rrim(I) all: 0.066 / Χ2: 0.936 / Net I/σ(I): 8.8 / Num. measured all: 370933
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.877.10.7153250.830.2870.7680.461100
1.87-1.967.80.45153970.940.1720.4830.479100
1.96-2.067.70.27453190.9710.1050.2940.52100
2.06-2.197.10.18753820.9830.0750.2020.576100
2.19-2.367.40.13153590.9910.0510.1410.645100
2.36-2.68.20.09654010.9950.0360.1030.767100
2.6-2.977.70.06854360.9970.0260.0731.146100
2.97-3.747.60.04854900.9990.0180.0511.79100
3.74-507.70.03957120.9990.0140.0421.90199.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FQH

4fqh


Resolution: 1.802→40.132 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.71
RfactorNum. reflection% reflection
Rfree0.2035 2359 4.84 %
Rwork0.1634 --
obs0.1654 48752 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 158.3 Å2 / Biso mean: 39.791 Å2 / Biso min: 16 Å2
Refinement stepCycle: final / Resolution: 1.802→40.132 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3392 0 12 456 3860
Biso mean--42.85 49.81 -
Num. residues----443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073698
X-RAY DIFFRACTIONf_angle_d1.0025073
X-RAY DIFFRACTIONf_chiral_restr0.061573
X-RAY DIFFRACTIONf_plane_restr0.006653
X-RAY DIFFRACTIONf_dihedral_angle_d17.3692244
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8022-1.83890.24941270.2303264197
1.8389-1.87890.22481360.1982684100
1.8789-1.92260.22231190.18612694100
1.9226-1.97070.21621310.18272702100
1.9707-2.0240.20841240.16252734100
2.024-2.08350.21641380.16612715100
2.0835-2.15080.22531460.16312670100
2.1508-2.22770.22431290.16952742100
2.2277-2.31680.21721390.1712683100
2.3168-2.42230.20411420.17462733100
2.4223-2.550.23671500.17982691100
2.55-2.70970.24011450.18472729100
2.7097-2.91890.23821510.18422735100
2.9189-3.21250.21921520.17342741100
3.2125-3.67710.20611420.15272766100
3.6771-4.63160.151390.13342805100
4.6316-40.1320.18721490.15672928100
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)
12.93310.7096-0.94612.4666-0.81622.389-0.08990.1946-0.242-0.096-0.0212-0.00160.3563-0.01850.06820.24280.00890.02770.202-0.02320.223411.0499-18.457111.091
22.0085-0.1575-0.11451.285-0.05211.6021-0.0055-0.2492-0.00130.2915-0.1143-0.0621-0.06860.15320.01480.29020.0053-0.03190.2328-0.01490.172415.4866-2.813818.2614
32.4969-0.5055-1.35381.83261.15493.6284-0.0766-0.4314-0.11460.69410.0292-0.23340.16610.38840.02050.3997-0.0134-0.11930.37370.03770.267425.66827.591524.1184
42.3607-0.4206-0.42273.5227-0.03041.923-0.01710.0829-0.12290.0547-0.08050.3540.017-0.23280.09790.1983-0.00270.03280.2213-0.030.2119-6.539-2.698515.2811
53.93770.0787-1.08692.28010.23131.71560.18640.04770.12050.169-0.062-0.4108-0.2710.2752-0.11470.3087-0.0772-0.00730.2932-0.01560.222321.333922.219117.0152
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain H and resid 1:97)H1 - 97
2X-RAY DIFFRACTION2(chain H and resid 98:133)H98 - 133
3X-RAY DIFFRACTION3(chain H and resid 134:214)H134 - 214
4X-RAY DIFFRACTION4(chain L and resid 1:106)L1 - 106
5X-RAY DIFFRACTION5(chain L and resid 107:213)L107 - 213

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