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- PDB-5wl2: VH1-69 germline antibody with CDR H3 sequence of CR9114 -

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Basic information

Entry
Database: PDB / ID: 5wl2
TitleVH1-69 germline antibody with CDR H3 sequence of CR9114
Components
  • Germline-reverted light chain of CR9114
  • Heavy chain of VH1-69 germline antibody with CDR H3 sequence of CR9114
KeywordsANTIVIRAL PROTEIN / VH1-69 germline antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsWilson, I.A. / Lang, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56 AI 117675 United States
CitationJournal: To Be Published
Title: Anti-idiotypic antibody K1-18 engages VH1-69 precursor and affinity-matured, anti-stem antibodies through mimicry of the HA stem.
Authors: Wilson, I.A. / Lang, S. / Kurosawa, Y. / Ohshima, N. / Ota, T. / Abadejos, J. / Lee, P.S. / Nemazee, D.
History
DepositionJul 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: Heavy chain of VH1-69 germline antibody with CDR H3 sequence of CR9114
L: Germline-reverted light chain of CR9114
A: Heavy chain of VH1-69 germline antibody with CDR H3 sequence of CR9114
B: Germline-reverted light chain of CR9114


Theoretical massNumber of molelcules
Total (without water)94,6194
Polymers94,6194
Non-polymers00
Water5,332296
1
H: Heavy chain of VH1-69 germline antibody with CDR H3 sequence of CR9114
L: Germline-reverted light chain of CR9114


Theoretical massNumber of molelcules
Total (without water)47,3092
Polymers47,3092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-23 kcal/mol
Surface area19570 Å2
MethodPISA
2
A: Heavy chain of VH1-69 germline antibody with CDR H3 sequence of CR9114
B: Germline-reverted light chain of CR9114


Theoretical massNumber of molelcules
Total (without water)47,3092
Polymers47,3092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-23 kcal/mol
Surface area19770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.125, 71.125, 185.705
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Antibody Heavy chain of VH1-69 germline antibody with CDR H3 sequence of CR9114


Mass: 24482.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Germline-reverted light chain of CR9114


Mass: 22827.123 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.87 Å3/Da / Density % sol: 57.09 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.095 M sodium citrate pH 5.6 19% 2-propanol 5% (v/v) glycerol 19% (w/v) PEG4000

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Data collection

DiffractionMean temperature: 77.2 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.89→43.663 Å / Num. obs: 81962 / % possible obs: 98.9 % / Redundancy: 4.5 % / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.03 / Rsym value: 0.07 / Net I/σ(I): 11.5
Reflection shellResolution: 1.89→1.96 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4107 / CC1/2: 0.61 / Rpim(I) all: 0.43 / Rsym value: 0.85 / % possible all: 97.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementResolution: 2→43.663 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2356 3652 5.27 %
Rwork0.1999 --
obs0.2017 69277 96.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→43.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6398 0 0 296 6694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096564
X-RAY DIFFRACTIONf_angle_d1.1118959
X-RAY DIFFRACTIONf_dihedral_angle_d13.513918
X-RAY DIFFRACTIONf_chiral_restr0.0641021
X-RAY DIFFRACTIONf_plane_restr0.0081142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9949-2.02110.31881530.29162300X-RAY DIFFRACTION88
2.0211-2.04880.31041720.27722379X-RAY DIFFRACTION92
2.0488-2.07810.32981140.27992353X-RAY DIFFRACTION91
2.0781-2.10910.32641530.27842394X-RAY DIFFRACTION92
2.1091-2.14210.30381590.25922433X-RAY DIFFRACTION94
2.1421-2.17720.33181280.26552447X-RAY DIFFRACTION94
2.1772-2.21470.25641150.24592469X-RAY DIFFRACTION93
2.2147-2.2550.3261220.25652438X-RAY DIFFRACTION95
2.255-2.29840.28411330.25362547X-RAY DIFFRACTION95
2.2984-2.34530.23281150.25592507X-RAY DIFFRACTION97
2.3453-2.39630.33361460.25872539X-RAY DIFFRACTION97
2.3963-2.4520.27281360.24342577X-RAY DIFFRACTION98
2.452-2.51330.29431960.24642495X-RAY DIFFRACTION98
2.5133-2.58130.31681520.25542562X-RAY DIFFRACTION100
2.5813-2.65720.31621600.25332620X-RAY DIFFRACTION100
2.6572-2.7430.35781210.25192631X-RAY DIFFRACTION100
2.743-2.8410.28221320.23092600X-RAY DIFFRACTION99
2.841-2.95470.23971420.22492601X-RAY DIFFRACTION99
2.9547-3.08910.24171600.23292579X-RAY DIFFRACTION100
3.0891-3.2520.31291350.21662581X-RAY DIFFRACTION98
3.252-3.45560.24511140.20642570X-RAY DIFFRACTION100
3.4556-3.72230.22941580.19732641X-RAY DIFFRACTION100
3.7223-4.09660.19151180.17862579X-RAY DIFFRACTION100
4.0966-4.68880.17591360.14172597X-RAY DIFFRACTION99
4.6888-5.90510.17351240.15132625X-RAY DIFFRACTION99
5.9051-43.67310.18821580.16922561X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -23.6452 Å / Origin y: 0.3136 Å / Origin z: -20.5317 Å
111213212223313233
T0.353 Å2-0.0328 Å20.076 Å2-0.3114 Å2-0.0434 Å2--0.373 Å2
L0.4434 °2-0.2753 °20.067 °2-0.1225 °2-0.0402 °2--0.692 °2
S0.0711 Å °-0.1044 Å °0.0338 Å °-0.1087 Å °-0.0558 Å °-0.0209 Å °0.075 Å °-0.0386 Å °-0.018 Å °
Refinement TLS groupSelection details: all

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