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- PDB-8fwf: Crystal structure of Apo form Fab235 -

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Basic information

Entry
Database: PDB / ID: 8fwf
TitleCrystal structure of Apo form Fab235
Components
  • Fab235, heavy chain
  • Fab235, light chain
KeywordsIMMUNE SYSTEM / HIV / membrane proximal external region / MPER / vaccine
Function / homologyACETATE ION / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsTan, K. / Kim, M. / Reinherz, E.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI145509 United States
CitationJournal: Nat Commun / Year: 2023
Title: Inadequate structural constraint on Fab approach rather than paratope elicitation limits HIV-1 MPER vaccine utility.
Authors: Tan, K. / Chen, J. / Kaku, Y. / Wang, Y. / Donius, L. / Khan, R.A. / Li, X. / Richter, H. / Seaman, M.S. / Walz, T. / Hwang, W. / Reinherz, E.L. / Kim, M.
History
DepositionJan 21, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Fab235, light chain
H: Fab235, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,57928
Polymers48,4712
Non-polymers2,10726
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8680 Å2
ΔGint-146 kcal/mol
Surface area19770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.755, 120.755, 86.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11H-519-

HOH

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody Fab235, light chain


Mass: 24203.967 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): 293 F cells
#2: Antibody Fab235, heavy chain


Mass: 24267.115 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): 293 F cells

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Non-polymers , 7 types, 267 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.29 Å3/Da / Density % sol: 62.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.0M Ammonium Sulphate, 0.1M HEPES:NaOH, 2%(v/v) PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2022
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 46067 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 25.75 Å2 / CC1/2: 0.985 / CC star: 0.996 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.065 / Rrim(I) all: 0.142 / Χ2: 1.42 / Net I/σ(I): 15.5
Reflection shellResolution: 1.94→1.97 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.973 / Mean I/σ(I) obs: 1.52 / Num. unique obs: 2312 / CC1/2: 0.505 / CC star: 0.819 / Rpim(I) all: 0.532 / Χ2: 0.734 / % possible all: 98.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→49.59 Å / SU ML: 0.1844 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.4853
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2057 2272 4.94 %
Rwork0.1705 43708 -
obs0.1722 45980 96.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.48 Å2
Refinement stepCycle: LAST / Resolution: 1.94→49.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3393 0 119 241 3753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013656
X-RAY DIFFRACTIONf_angle_d1.04194976
X-RAY DIFFRACTIONf_chiral_restr0.0692546
X-RAY DIFFRACTIONf_plane_restr0.012629
X-RAY DIFFRACTIONf_dihedral_angle_d9.2407523
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.990.26671380.22652576X-RAY DIFFRACTION92
1.99-2.030.25541230.20452766X-RAY DIFFRACTION98.63
2.03-2.080.21281380.19882765X-RAY DIFFRACTION98.14
2.08-2.140.2461580.18652701X-RAY DIFFRACTION98.01
2.14-2.20.20711470.18272738X-RAY DIFFRACTION97.83
2.2-2.270.22961420.17742739X-RAY DIFFRACTION97.56
2.27-2.350.21171390.1772738X-RAY DIFFRACTION97.36
2.35-2.450.2311410.18052731X-RAY DIFFRACTION97.13
2.45-2.560.25131420.18762743X-RAY DIFFRACTION96.78
2.56-2.70.24661210.19362734X-RAY DIFFRACTION96.55
2.7-2.860.2271490.18312746X-RAY DIFFRACTION96.66
2.86-3.090.21741650.17932726X-RAY DIFFRACTION96.85
3.09-3.40.19461340.17072759X-RAY DIFFRACTION96.69
3.4-3.890.18921410.1542750X-RAY DIFFRACTION95.13
3.89-4.90.15711480.13282718X-RAY DIFFRACTION93.45
4.9-49.590.1931460.16682778X-RAY DIFFRACTION90.5
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)
12.67253150130.206508193840.5010065828211.96057445017-0.4400082836992.51293584659-0.101462835546-0.05678137224020.475933776470.11365958448-0.00737467659399-0.0991482861368-0.3849024606260.02610294591940.09515736132150.246612473653-0.002220433305690.01912834081970.120947624573-0.02068891720660.2408630833132.6753784469535.99437000312.80049356682
23.28199888941-0.01104559186541.735374771450.08407866816630.1351106179081.13160438437-0.11411440649-0.1631564644410.3199944656450.1036271838280.0470064449045-0.080812803486-0.1727518661990.01264570147840.04014515258860.26275185153-0.03993211524710.00609048779440.195005377693-0.04752039396550.24330003284517.975141494827.896396719811.780699817
32.78153552371-1.148493165910.4952411213765.723382789910.3489975247571.70241485823-0.074243947430.1656861122040.0409761640728-0.2293999538470.121746630155-0.427546143157-0.05143359029340.30295664429-0.0357914302330.231996496674-0.0884655424759-0.001419830348970.303710408577-0.08601785084690.25206980995538.520531170721.889266136716.34407494
42.25795999419-1.432832128350.340948268553.13760902901-0.08039986233490.8625800295760.0226987698288-0.3107472594470.3536376966230.3188291995250.0562670174308-0.39110576218-0.09247749612810.0317473665721-0.08477698623010.198968662319-0.02010225889020.03973762302320.211461158019-0.03666254580270.1613473614730.24888662543215.221243890914.709409222
51.73815675361-0.3608324737460.7495393376981.98989914514-0.3141219999431.088198943260.0414910791623-0.06766275870740.08969802201860.1134716788460.008767378113570.0604532483093-0.0839685007299-0.123023590096-0.05103877832390.159237320009-0.005617210529920.05096237724580.14895559899-0.02347918405850.108571467978-3.8389542924415.85694879449.1732974712
60.9586690942090.6049966856790.7967190779460.9757221231660.2934082574620.7060850438760.111625015992-0.3464429667430.3558619827330.248898188695-0.2874476200920.1834806236450.100679368695-0.1847168839370.1545026593040.260643718489-0.0611893207425-0.007756704950550.338012188951-0.1322657332410.27958410167227.155894620418.048893328224.8813349084
74.321086976272.483617644672.368551013545.080248969952.905251152923.454756795450.593906397125-0.710856580362-0.08349039452110.894341683197-0.45040366617-0.2365527773420.395984861008-0.201461086051-0.02007348073130.469853164693-0.1774060699960.05010845997750.536691051837-0.1128518529060.30092652089326.23283687717.003050171333.9447948892
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'L' and (resid 1 through 81 )LA1 - 811 - 81
22chain 'L' and (resid 82 through 134 )LA82 - 13482 - 134
33chain 'L' and (resid 135 through 220 )LA135 - 220135 - 220
44chain 'H' and (resid 1 through 44 )HB1 - 441 - 44
55chain 'H' and (resid 45 through 121 )HB45 - 12145 - 121
66chain 'H' and (resid 122 through 198 )HB122 - 198122 - 198
77chain 'H' and (resid 199 through 226 )HB199 - 226199 - 226

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