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- PDB-3eot: Crystal structure of LAC031, an engineered anti-VLA1 Fab -

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Basic information

Entry
Database: PDB / ID: 3eot
TitleCrystal structure of LAC031, an engineered anti-VLA1 Fab
Components
  • FAB FRAGMENT, HEAVY CHAIN
  • FAB FRAGMENT, LIGHT CHAIN
KeywordsIMMUNE SYSTEM / antibody / Fab / VLA-1 / domain swap / proten engineering
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsBoriack-Sjodin, P.A. / Clark, L.A.
CitationJournal: Protein Eng.Des.Sel. / Year: 2009
Title: An antibody loop replacement design feasibility study and a loop-swapped dimer structure.
Authors: Clark, L.A. / Boriack-Sjodin, P.A. / Day, E. / Eldredge, J. / Fitch, C. / Jarpe, M. / Miller, S. / Li, Y. / Simon, K. / van Vlijmen, H.W.
History
DepositionSep 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 30, 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
H: FAB FRAGMENT, HEAVY CHAIN
L: FAB FRAGMENT, LIGHT CHAIN


Theoretical massNumber of molelcules
Total (without water)47,7392
Polymers47,7392
Non-polymers00
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-25 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.163, 132.425, 41.827
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Antibody FAB FRAGMENT, HEAVY CHAIN


Mass: 24224.074 Da / Num. of mol.: 1 / Mutation: W92I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody FAB FRAGMENT, LIGHT CHAIN


Mass: 23514.824 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)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.41 Å3/Da / Density % sol: 49.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16-20% Peg 3350, 100 mM Na Cacodylate, 200 mM MgCl2 , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 36217 / % possible obs: 96.3 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.06 / Χ2: 1.169 / Net I/σ(I): 35.365
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.9-1.975.80.21828990.52979
1.97-2.056.10.17133300.56989.9
2.05-2.146.50.15435090.59294.7
2.14-2.256.70.13736860.62599.3
2.25-2.397.10.12237100.687100
2.39-2.587.20.10137460.833100
2.58-2.847.10.08537431.239100
2.84-3.2570.06537791.707100
3.25-4.096.80.04938202.1100
4.09-506.90.04139952.26999.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
CBASSdata collection
AMoREphasing
RefinementResolution: 1.9→35 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.792 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1780 4.8 %RANDOM
Rwork0.234 ---
obs0.236 35959 96.5 %-
all-37281 --
Displacement parametersBiso max: 66.08 Å2 / Biso mean: 34.008 Å2 / Biso min: 14.28 Å2
Baniso -1Baniso -2Baniso -3
1-3.108 Å20 Å20 Å2
2--12.76 Å20 Å2
3----15.869 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.9→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3243 0 0 204 3447
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4941.5
X-RAY DIFFRACTIONc_scbond_it2.1112
X-RAY DIFFRACTIONc_mcangle_it2.3092
X-RAY DIFFRACTIONc_scangle_it3.022.5
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_improper_angle_d0.6
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1MSI_CNX_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2MSI_CNX_TOPPAR:ion.param
X-RAY DIFFRACTION3MSI_CNX_TOPPAR:water_rep.param

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