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- PDB-5f7e: Crystal structure of germ-line precursor of 3BNC60 Fab -

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Basic information

Entry
Database: PDB / ID: 5f7e
TitleCrystal structure of germ-line precursor of 3BNC60 Fab
Components
  • Fab heavy chain
  • Fab light chain
KeywordsIMMUNE SYSTEM / ANTIBODY / HIV-1
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSievers, S.A. / Scharf, L. / Jiang, S. / Bjorkman, P.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HIVRAD P01 AI100148 United States
Bill & Melinda Gates Foundation1040753 United States
CitationJournal: Elife / Year: 2016
Title: Structural basis for germline antibody recognition of HIV-1 immunogens.
Authors: Scharf, L. / West, A.P. / Sievers, S.A. / Chen, C. / Jiang, S. / Gao, H. / Gray, M.D. / McGuire, A.T. / Scheid, J.F. / Nussenzweig, M.C. / Stamatatos, L. / Bjorkman, P.J.
History
DepositionDec 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Fab heavy chain
L: Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,1892
Polymers48,1892
Non-polymers00
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-24 kcal/mol
Surface area18500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.857, 74.857, 83.113
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Fab heavy chain


Mass: 25166.172 Da / Num. of mol.: 1 / Fragment: 3BNC60 germline heavy chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human)
#2: Antibody Fab light chain


Mass: 23022.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9.1 / Details: 0.1 M Bicine pH 9.1, 10% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.9→36.327 Å / Num. all: 37312 / Num. obs: 37312 / % possible obs: 99.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 25.01 Å2 / Rpim(I) all: 0.038 / Rrim(I) all: 0.099 / Rsym value: 0.091 / Net I/av σ(I): 8.267 / Net I/σ(I): 16.1 / Num. measured all: 243616
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.9-26.50.80313434753110.3390.8032.698.5
2-2.126.40.5391.43241150930.230.5393.899.8
2.12-2.276.80.38623247047900.1590.3865.399.7
2.27-2.456.50.292.72916044840.1220.296.899.8
2.45-2.696.60.1894.12708841350.0790.1899.899.8
2.69-36.70.1166.72533737570.0480.11615.599.8
3-3.476.40.0612.82145033260.0250.0626.899.7
3.47-4.256.70.035211921528560.0140.03544.599.9
4.25-6.016.30.02626.51418922480.0110.02655.299.7
6.01-36.3276.10.02523.9794913120.0110.02556.699.1

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Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHENIX1.10pre_2135refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JDV

4jdv


Resolution: 1.9→36.327 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2137 1509 4.24 %Random selection
Rwork0.199 34079 --
obs0.1996 35588 94.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.8 Å2 / Biso mean: 33.0684 Å2 / Biso min: 15.51 Å2
Refinement stepCycle: final / Resolution: 1.9→36.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3221 0 0 281 3502
Biso mean---44.42 -
Num. residues----428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113302
X-RAY DIFFRACTIONf_angle_d1.3634505
X-RAY DIFFRACTIONf_chiral_restr0.082508
X-RAY DIFFRACTIONf_plane_restr0.006578
X-RAY DIFFRACTIONf_dihedral_angle_d14.9121170
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9001-1.96150.31491360.28133172330898
1.9615-2.03160.28871400.26183167330798
2.0316-2.11290.30451410.24333125326698
2.1129-2.20910.22451340.22353154328898
2.2091-2.32550.23421410.21823136327797
2.3255-2.47120.25471390.21913099323897
2.4712-2.66190.21861410.21363104324595
2.6619-2.92970.24761290.19822976310592
2.9297-3.35340.19721320.18162962309491
3.3534-4.2240.16721370.16813055319292
4.224-37.43570.1881390.18173129326890
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)
10.80920.34380.2581.7342-0.02570.7803-0.0287-0.0272-0.0230.023-0.0059-0.0436-0.0736-0.04950.04210.1758-0.0120.0010.19330.00060.1712-8.6117-17.600920.6709
20.1785-0.06050.1180.7998-0.14010.6222-0.0120.0403-0.0239-0.02410.013-0.0699-0.0224-0.07680.00580.13670.00820.00310.1722-0.01210.1497-5.9577-5.54534.86
30.6094-0.32170.82790.5964-0.07932.4605-0.0218-0.11530.0367-0.04330.09650.0685-0.024-0.5552-0.05520.2253-0.0173-0.01710.2910.03080.2111-9.42877.328-3.9396
41.1127-0.03660.57350.69510.46072.3659-0.03760.0306-0.0204-0.032-0.0361-0.00750.40810.39620.18160.31660.01640.05570.30290.0170.28566.9579-23.6428-4.199
50.7616-1.23641.61922.6969-3.27944.04120.01270.04370.0572-0.1007-0.0815-0.12490.03520.260.0840.24810.00050.01540.2006-0.01810.21014.2501-30.17795.7609
60.75680.6563-0.21991.6116-0.0081.76330.0590.0649-0.0647-0.0546-0.00550.10680.2912-0.0206-0.06320.25160.00870.01790.20230.01890.1983-2.8733-30.37970.1381
70.34560.3767-0.51021.1127-0.09470.9325-0.04790.0212-0.042-0.24110.0287-0.03820.29340.00120.04620.23450.01920.00430.2134-0.01920.22211.5227-20.6047-3.4589
81.5796-1.3287-0.39181.85130.51442.09070.01580.00620.29070.01930.0465-0.3596-0.22890.1702-0.05560.258-0.02620.00350.21630.00380.25637.28967.3541-7.4557
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 91 )H0
2X-RAY DIFFRACTION2chain 'H' and (resid 92 through 151 )H0
3X-RAY DIFFRACTION3chain 'H' and (resid 152 through 215 )H0
4X-RAY DIFFRACTION4chain 'L' and (resid 2 through 18 )L0
5X-RAY DIFFRACTION5chain 'L' and (resid 19 through 38 )L0
6X-RAY DIFFRACTION6chain 'L' and (resid 39 through 75 )L0
7X-RAY DIFFRACTION7chain 'L' and (resid 76 through 109 )L0
8X-RAY DIFFRACTION8chain 'L' and (resid 110 through 208 )L0

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