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- PDB-4lri: Anti CMV Fab Fragment -

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Basic information

Entry
Database: PDB / ID: 4lri
TitleAnti CMV Fab Fragment
Components
  • MSL-109 Heavy Chain
  • MSL-109 Light Chain
KeywordsIMMUNE SYSTEM / Fab Fragment / CMV neutralizing antibody / glycoprotein H or gH from CMV
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsStengel, K.F.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Mechanism for neutralizing activity by the anti-CMV gH/gL monoclonal antibody MSL-109.
Authors: Fouts, A.E. / Comps-Agrar, L. / Stengel, K.F. / Ellerman, D. / Schoeffler, A.J. / Warming, S. / Eaton, D.L. / Feierbach, B.
History
DepositionJul 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: MSL-109 Light Chain
B: MSL-109 Light Chain
P: MSL-109 Heavy Chain
C: MSL-109 Heavy Chain


Theoretical massNumber of molelcules
Total (without water)97,8074
Polymers97,8074
Non-polymers00
Water12,773709
1
A: MSL-109 Light Chain
P: MSL-109 Heavy Chain


Theoretical massNumber of molelcules
Total (without water)48,9032
Polymers48,9032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-25 kcal/mol
Surface area19410 Å2
MethodPISA
2
B: MSL-109 Light Chain
C: MSL-109 Heavy Chain


Theoretical massNumber of molelcules
Total (without water)48,9032
Polymers48,9032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-24 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.619, 101.649, 113.794
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody MSL-109 Light Chain


Mass: 24006.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody MSL-109 Heavy Chain


Mass: 24896.662 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 709 / 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: 2.18 Å3/Da / Density % sol: 43.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1mM Hepes pH 7.5, 70% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→40 Å / Num. obs: 102913 / % possible obs: 100 %

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→29.112 Å / SU ML: 0.17 / σ(F): 1.34 / Phase error: 20.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2125 5147 5 %
Rwork0.187 --
obs0.1883 102913 99.83 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.261 Å2 / ksol: 0.316 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.9132 Å20 Å2-0 Å2
2--3.3272 Å2-0 Å2
3----2.4141 Å2
Refinement stepCycle: LAST / Resolution: 1.65→29.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6698 0 0 709 7407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076861
X-RAY DIFFRACTIONf_angle_d1.1679321
X-RAY DIFFRACTIONf_dihedral_angle_d12.9212447
X-RAY DIFFRACTIONf_chiral_restr0.0841049
X-RAY DIFFRACTIONf_plane_restr0.0051193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.66910.25371610.233097X-RAY DIFFRACTION96
1.6691-1.68870.25411680.22133205X-RAY DIFFRACTION100
1.6887-1.70930.27791770.21443238X-RAY DIFFRACTION100
1.7093-1.73090.26621570.20913217X-RAY DIFFRACTION100
1.7309-1.75370.24451740.20493270X-RAY DIFFRACTION100
1.7537-1.77770.23751580.19653194X-RAY DIFFRACTION100
1.7777-1.80310.25381790.20043244X-RAY DIFFRACTION100
1.8031-1.830.23571710.19623214X-RAY DIFFRACTION100
1.83-1.85860.23961740.19573218X-RAY DIFFRACTION100
1.8586-1.88910.23871990.1893217X-RAY DIFFRACTION100
1.8891-1.92160.2471830.19523203X-RAY DIFFRACTION100
1.9216-1.95660.22711620.18833282X-RAY DIFFRACTION100
1.9566-1.99420.20661770.19423251X-RAY DIFFRACTION100
1.9942-2.03490.25881640.19193233X-RAY DIFFRACTION100
2.0349-2.07910.21391560.1923251X-RAY DIFFRACTION100
2.0791-2.12750.20041550.18853257X-RAY DIFFRACTION100
2.1275-2.18070.22811890.19013224X-RAY DIFFRACTION100
2.1807-2.23960.22571820.19033260X-RAY DIFFRACTION100
2.2396-2.30550.24381640.19923258X-RAY DIFFRACTION100
2.3055-2.37990.23291790.20213260X-RAY DIFFRACTION100
2.3799-2.46490.26021750.20933251X-RAY DIFFRACTION100
2.4649-2.56350.25961710.2113260X-RAY DIFFRACTION100
2.5635-2.68010.24682010.21153248X-RAY DIFFRACTION100
2.6801-2.82130.23491740.21183272X-RAY DIFFRACTION100
2.8213-2.99790.2161600.2063294X-RAY DIFFRACTION100
2.9979-3.22910.20691620.18363313X-RAY DIFFRACTION100
3.2291-3.55350.19741720.17363299X-RAY DIFFRACTION100
3.5535-4.06650.16061760.16333354X-RAY DIFFRACTION100
4.0665-5.11890.15121380.14673384X-RAY DIFFRACTION100
5.1189-29.11640.19661890.18993498X-RAY DIFFRACTION100

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