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- PDB-6v4r: Crystal structure of a chimeric MR78-like antibody chimera-1 Fab -

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Basic information

Entry
Database: PDB / ID: 6v4r
TitleCrystal structure of a chimeric MR78-like antibody chimera-1 Fab
Components
  • Chimera-1 Fab heavy chain
  • Chimera-1 Fab light chain
KeywordsIMMUNE SYSTEM / Marburg Virus / antibody
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.48 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
Revision 1.4Oct 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: Chimera-1 Fab heavy chain
L: Chimera-1 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,4952
Polymers47,4952
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-24 kcal/mol
Surface area18950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.780, 133.780, 91.910
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Antibody Chimera-1 Fab heavy chain


Mass: 23967.701 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 Chimera-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
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: 5 Å3/Da / Density % sol: 75.39 % / Mosaicity: 0.284 °
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 4.5 M NaCl, 0.1 M HEPES, 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: Nov 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.48→57.93 Å / Num. obs: 12393 / % possible obs: 99.2 % / Redundancy: 16.6 % / Biso Wilson estimate: 145.12 Å2 / Rpim(I) all: 0.084 / Rrim(I) all: 0.342 / Net I/σ(I): 8.8 / Num. measured all: 206074
Reflection shellResolution: 3.48→3.54 Å / Redundancy: 17.3 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 618 / Rpim(I) all: 0.995 / Rrim(I) all: 4.159 / % possible all: 98.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.563
Highest resolutionLowest resolution
Rotation57.93 Å3.99 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
xia2data reduction
PHENIXRosetta-Phenixrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JRP

5jrp


Resolution: 3.48→57.93 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.891 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.608
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3273 524 4.2 %RANDOM
Rwork0.2946 ---
obs0.2961 11852 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 284.51 Å2 / Biso mean: 172.603 Å2 / Biso min: 107.51 Å2
Baniso -1Baniso -2Baniso -3
1-6.54 Å23.27 Å20 Å2
2--6.54 Å2-0 Å2
3----21.21 Å2
Refinement stepCycle: final / Resolution: 3.48→57.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3259 0 0 0 3259
Num. residues----430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0133342
X-RAY DIFFRACTIONr_bond_other_d0.0360.0172963
X-RAY DIFFRACTIONr_angle_refined_deg2.1781.6434556
X-RAY DIFFRACTIONr_angle_other_deg2.4331.5686940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.185427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.54624.091132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.52715525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.47157
X-RAY DIFFRACTIONr_chiral_restr0.1150.2448
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023720
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02657
X-RAY DIFFRACTIONr_mcbond_it14.15618.6521717
X-RAY DIFFRACTIONr_mcbond_other14.16318.651715
X-RAY DIFFRACTIONr_mcangle_it19.23927.972141
LS refinement shellResolution: 3.48→3.57 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.513 27 -
Rwork0.485 863 -
all-890 -
obs--98.67 %

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