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- PDB-6v4q: Crystal structure of a MR78-like antibody naive-1 Fab -

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Basic information

Entry
Database: PDB / ID: 6v4q
TitleCrystal structure of a MR78-like antibody naive-1 Fab
Components
  • Naive-1 Fab heavy chain
  • Naive-1 Fab light chain
KeywordsIMMUNE SYSTEM / Marburg Virus / antibody
Function / homologyISOPROPYL ALCOHOL
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.39 Å
AuthorsBozhanova, N.G. / Crowe, J.E. / Meiler, J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI117905 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI141661 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21 AI21799 Ebola United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Discovery of Marburg virus neutralizing antibodies from virus-naive human antibody repertoires using large-scale structural predictions.
Authors: Bozhanova, N.G. / Sangha, A.K. / Sevy, A.M. / Gilchuk, P. / Huang, K. / Nargi, R.S. / Reidy, J.X. / Trivette, A. / Carnahan, R.H. / Bukreyev, A. / Crowe Jr., J.E. / Meiler, J.
History
DepositionNov 28, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Dec 23, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 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

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Assembly

Deposited unit
H: Naive-1 Fab heavy chain
L: Naive-1 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2018
Polymers47,6802
Non-polymers5216
Water9,080504
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-32 kcal/mol
Surface area20140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.980, 73.120, 105.160
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 Naive-1 Fab heavy chain


Mass: 24153.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / Strain (production host): Expi293F
#2: Antibody Naive-1 Fab light chain


Mass: 23527.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / Strain (production host): Expi293F
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 504 / 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: 2.58 Å3/Da / Density % sol: 52.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1% w/v PEG 8000, 20% v/v 2-Propanol, 0.1 M Tris, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.39→43.78 Å / Num. obs: 99126 / % possible obs: 99.4 % / Redundancy: 5 % / Biso Wilson estimate: 11.256 Å2 / Rpim(I) all: 0.025 / Rrim(I) all: 0.058 / Net I/σ(I): 16 / Num. measured all: 495046
Reflection shellResolution: 1.39→1.41 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.4 / Num. unique obs: 4511 / Rpim(I) all: 0.245 / Rrim(I) all: 0.4 / % possible all: 92

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.392
Highest resolutionLowest resolution
Rotation43.78 Å1.66 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W72

1w72


Resolution: 1.39→43.78 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.054
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1872 4880 4.9 %RANDOM
Rwork0.1647 ---
obs0.1658 94164 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 67.13 Å2 / Biso mean: 15.089 Å2 / Biso min: 8.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0 Å2-0 Å2
2---0.16 Å2-0 Å2
3---0.32 Å2
Refinement stepCycle: final / Resolution: 1.39→43.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3304 0 34 504 3842
Biso mean--24.93 25.99 -
Num. residues----434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0133503
X-RAY DIFFRACTIONr_bond_other_d0.0360.0173111
X-RAY DIFFRACTIONr_angle_refined_deg1.9531.6414784
X-RAY DIFFRACTIONr_angle_other_deg2.4321.577294
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4595463
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40323.49149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.39115556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6381511
X-RAY DIFFRACTIONr_chiral_restr0.1030.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023926
X-RAY DIFFRACTIONr_gen_planes_other0.0140.02715
X-RAY DIFFRACTIONr_mcbond_it1.5111.3831765
X-RAY DIFFRACTIONr_mcbond_other1.5041.3811764
X-RAY DIFFRACTIONr_mcangle_it2.292.0722209
LS refinement shellResolution: 1.39→1.426 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 325 -
Rwork0.227 6457 -
all-6782 -
obs--93.17 %

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