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- PDB-5weq: The crystal structure of a MR78 mutant -

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Basic information

Entry
Database: PDB / ID: 5weq
TitleThe crystal structure of a MR78 mutant
Components
  • MR78 mutant Fab heavy chain
  • MR78 mutant light chain
KeywordsIMMUNE SYSTEM / Marburg Virus / Antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsDong, J. / Williamson, L.E. / Crowe, J.E.
CitationJournal: Structure / Year: 2017
Title: Role of Non-local Interactions between CDR Loops in Binding Affinity of MR78 Antibody to Marburg Virus Glycoprotein.
Authors: Sangha, A.K. / Dong, J. / Williamson, L. / Hashiguchi, T. / Saphire, E.O. / Crowe, J.E. / Meiler, J.
History
DepositionJul 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
A: MR78 mutant light chain
B: MR78 mutant Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)47,3482
Polymers47,3482
Non-polymers00
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-24 kcal/mol
Surface area19490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.177, 117.177, 92.104
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-344-

HOH

21B-358-

HOH

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Components

#1: Antibody MR78 mutant light chain


Mass: 23494.041 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody MR78 mutant Fab heavy chain


Mass: 23853.578 Da / Num. of mol.: 1
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.: 200 / 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: 3.65 Å3/Da / Density % sol: 66.33 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 4.0 - 4.5 M NaCl, 0.1 M HEPES, pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 50000 / % possible obs: 99.6 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 9.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2→49.434 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.01
RfactorNum. reflection% reflection
Rfree0.2152 2448 4.91 %
Rwork0.1858 --
obs0.1873 49808 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→49.434 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3266 0 0 200 3466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083395
X-RAY DIFFRACTIONf_angle_d0.894634
X-RAY DIFFRACTIONf_dihedral_angle_d5.692729
X-RAY DIFFRACTIONf_chiral_restr0.058520
X-RAY DIFFRACTIONf_plane_restr0.006590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9923-2.0330.36011110.31832563X-RAY DIFFRACTION92
2.033-2.07720.3531490.28132750X-RAY DIFFRACTION99
2.0772-2.12550.31461210.26262796X-RAY DIFFRACTION99
2.1255-2.17870.28551240.24482747X-RAY DIFFRACTION99
2.1787-2.23760.26931470.24162755X-RAY DIFFRACTION99
2.2376-2.30350.25611530.2332790X-RAY DIFFRACTION99
2.3035-2.37780.26611350.21832772X-RAY DIFFRACTION100
2.3778-2.46280.2921500.22192754X-RAY DIFFRACTION100
2.4628-2.56140.29291530.22872808X-RAY DIFFRACTION100
2.5614-2.67790.23831540.2362758X-RAY DIFFRACTION100
2.6779-2.81910.26211380.22662805X-RAY DIFFRACTION100
2.8191-2.99570.25481670.22032790X-RAY DIFFRACTION100
2.9957-3.2270.24361230.20962838X-RAY DIFFRACTION100
3.227-3.55170.21361450.17442827X-RAY DIFFRACTION100
3.5517-4.06540.17031570.14892808X-RAY DIFFRACTION100
4.0654-5.12110.16381430.12882869X-RAY DIFFRACTION100
5.1211-49.44970.18571780.16992930X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -42.9384 Å / Origin y: 29.6277 Å / Origin z: -33.2857 Å
111213212223313233
T0.2758 Å2-0.0588 Å2-0.0131 Å2-0.4059 Å2-0.0201 Å2--0.2789 Å2
L0.3957 °2-0.3599 °20.1331 °2-2.0384 °2-0.8237 °2--2.0765 °2
S-0.0282 Å °0.0728 Å °-0.0099 Å °-0.0885 Å °-0.0187 Å °-0.0872 Å °0.0938 Å °0.129 Å °0.0596 Å °
Refinement TLS groupSelection details: all

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