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- PDB-5u3p: Crystal Structure of DH511.4 Fab -

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Basic information

Entry
Database: PDB / ID: 5u3p
TitleCrystal Structure of DH511.4 Fab
Components
  • DH511.4 Fab Heavy Chain
  • DH511.4 Fab Light Chain
KeywordsIMMUNE SYSTEM / HIV-1 / Neutralizing / Antibody / gp41 / MPER
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsNicely, N.I. / Williams, L.D. / Ofek, G. / Haynes, B.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI 0100645 United States
CitationJournal: Sci Immunol / Year: 2017
Title: Potent and broad HIV-neutralizing antibodies in memory B cells and plasma.
Authors: Williams, L.D. / Ofek, G. / Schatzle, S. / McDaniel, J.R. / Lu, X. / Nicely, N.I. / Wu, L. / Lougheed, C.S. / Bradley, T. / Louder, M.K. / McKee, K. / Bailer, R.T. / O'Dell, S. / Georgiev, I. ...Authors: Williams, L.D. / Ofek, G. / Schatzle, S. / McDaniel, J.R. / Lu, X. / Nicely, N.I. / Wu, L. / Lougheed, C.S. / Bradley, T. / Louder, M.K. / McKee, K. / Bailer, R.T. / O'Dell, S. / Georgiev, I.S. / Seaman, M.S. / Parks, R.J. / Marshall, D.J. / Anasti, K. / Yang, G. / Nie, X. / Tumba, N.L. / Wiehe, K. / Wagh, K. / Korber, B. / Kepler, T.B. / Munir Alam, S. / Morris, L. / Kamanga, G. / Cohen, M.S. / Bonsignori, M. / Xia, S.M. / Montefiori, D.C. / Kelsoe, G. / Gao, F. / Mascola, J.R. / Moody, M.A. / Saunders, K.O. / Liao, H.X. / Tomaras, G.D. / Georgiou, G. / Haynes, B.F.
History
DepositionDec 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.2Aug 23, 2017Group: Author supporting evidence / Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / pdbx_audit_support / software
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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: DH511.4 Fab Heavy Chain
L: DH511.4 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)48,4002
Polymers48,4002
Non-polymers00
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-22 kcal/mol
Surface area20720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.486, 48.163, 57.129
Angle α, β, γ (deg.)86.140, 82.320, 82.290
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody DH511.4 Fab Heavy Chain


Mass: 25051.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#2: Antibody DH511.4 Fab Light Chain


Mass: 23348.740 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293 / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.37 Å3/Da / Density % sol: 48.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M di-sodium hydrogen phosphate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→27.287 Å / Num. obs: 65896 / % possible obs: 93.3 % / Redundancy: 2.5 % / Biso Wilson estimate: 18.96 Å2 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.048 / Rrim(I) all: 0.076 / Χ2: 1.353 / Net I/σ(I): 15.1 / Num. measured all: 165642
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Diffraction-ID% possible all
1.5-1.532.30.42432300.746193.1
1.53-1.552.50.3960.805194.4
1.55-1.582.50.3550.852194.1
1.58-1.622.60.3110.889194.9
1.62-1.652.60.2790.906194.8
1.65-1.692.60.2330.932194.6
1.69-1.732.60.2030.938195.1
1.73-1.782.60.1630.96195.1
1.78-1.832.60.140.969195.1
1.83-1.892.60.1180.973195.3
1.89-1.962.60.0990.981194.9
1.96-2.042.60.0810.984194.8
2.04-2.132.50.0720.988194.9
2.13-2.242.50.0650.99195.6
2.24-2.382.50.0610.989195.6
2.38-2.562.50.0580.988195.9
2.56-2.822.50.0510.991195.2
2.82-3.232.40.0460.992194.9
3.23-4.072.20.0430.992190.6
4.07-5020.0420.992166.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GHB, 4KMT

3ghb

4kmt


Resolution: 1.5→27.287 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 20.7
RfactorNum. reflection% reflection
Rfree0.2111 1964 3.05 %
Rwork0.188 --
obs0.1887 64453 90.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 103 Å2 / Biso mean: 28.2843 Å2 / Biso min: 13.77 Å2
Refinement stepCycle: final / Resolution: 1.5→27.287 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3406 0 0 191 3597
Biso mean---31.27 -
Num. residues----446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063559
X-RAY DIFFRACTIONf_angle_d1.1214844
X-RAY DIFFRACTIONf_chiral_restr0.075545
X-RAY DIFFRACTIONf_plane_restr0.005622
X-RAY DIFFRACTIONf_dihedral_angle_d12.9711269
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.53440.20041130.20213438355169
1.5344-1.57590.21761390.20254361450088
1.5759-1.62220.20081390.19524474461390
1.6222-1.67460.24831390.19454505464491
1.6746-1.73440.19491440.18614542468692
1.7344-1.80390.21371460.18674654480094
1.8039-1.88590.21451450.18744632477794
1.8859-1.98530.21481470.19034687483494
1.9853-2.10970.22811470.18564704485195
2.1097-2.27250.19181490.19124739488895
2.2725-2.50110.23231480.2024748489696
2.5011-2.86260.23241490.20384733488296
2.8626-3.60530.20541460.18444658480494
3.6053-27.29180.19241130.17073614372773
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)
11.6176-0.5829-0.14171.50280.12452.283-0.01880.0299-0.124-0.02210.0737-0.07340.083-0.0103-0.070.145-0.01440.00830.14170.00520.18161.3074-39.6683-130.187
20.6147-0.0893-0.13680.629-0.14090.8032-0.08480.03310.0135-0.0407-0.0022-0.02270.01230.01820.13190.1469-0.0178-0.0180.16290.01960.178-1.9289-28.2157-131.8104
31.1394-0.72110.19541.296-0.45511.192-0.1468-0.150.02780.07440.17570.12410.0041-0.1425-0.01590.18880.0246-0.00210.18790.00190.1702-21.0576-13.1879-115.2607
41.7094-1.52770.76916.0171-1.53220.49930.0473-0.0939-0.14250.28130.00930.3272-0.0928-0.5631-0.02410.3370.07490.05940.34220.0290.2037-23.5829-20.2602-107.9116
51.7099-0.93250.17542.32310.10671.75560.01430.08350.0313-0.0746-0.0637-0.1111-0.128-0.00850.04390.1581-0.01560.01260.15730.00490.1581-0.3826-22.1558-144.6801
61.195-0.45110.53331.1981-0.63791.8004-0.1217-0.07190.17130.2472-0.0152-0.1887-0.250.19460.0770.22270.0077-0.04980.1752-0.00970.2064-10.7744-4.034-118.7542
71.1654-0.39121.09940.77440.22545.25620.0341-0.15210.07510.141-0.0645-0.00510.2277-0.02710.00790.2023-0.0181-0.02940.1907-0.01150.1785-13.1245-10.0551-122.6739
81.7185-0.13980.26871.8757-0.20094.2797-0.1237-0.18130.31620.60620.0662-0.2436-0.56060.25260.0080.4149-0.052-0.10820.247-0.02280.3196-8.33493.2673-115.2383
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain H and resid 1:95)H1 - 95
2X-RAY DIFFRACTION2(chain H and resid 96:129)H96 - 129
3X-RAY DIFFRACTION3(chain H and resid 130:198)H130 - 198
4X-RAY DIFFRACTION4(chain H and resid 199:213)H199 - 213
5X-RAY DIFFRACTION5(chain L and resid 1:105)L1 - 105
6X-RAY DIFFRACTION6(chain L and resid 106:160)L106 - 160
7X-RAY DIFFRACTION7(chain L and resid 161:184)L161 - 184
8X-RAY DIFFRACTION8(chain L and resid 185:212)L185 - 212

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