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- PDB-2fat: An anti-urokinase plasminogen activator receptor (UPAR) antibody:... -

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Basic information

Entry
Database: PDB / ID: 2fat
TitleAn anti-urokinase plasminogen activator receptor (UPAR) antibody: Crystal structure and binding epitope
Components
  • FAB ATN-615, heavy chain
  • FAB ATN-615, light chain
KeywordsIMMUNE SYSTEM / ANTI-UPAR ANTIBODY / ATN-615 / FAB
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsLi, Y. / Parry, G. / Shi, X. / Chen, L. / Callahan, J.A. / Mazar, A.P. / Huang, M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: An anti-urokinase plasminogen activator receptor (uPAR) antibody: crystal structure and binding epitope
Authors: Li, Y. / Parry, G. / Chen, L. / Callahan, J.A. / Shaw, D.E. / Meehan, E.J. / Mazar, A.P. / Huang, M.
History
DepositionDec 7, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 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
L: FAB ATN-615, light chain
H: FAB ATN-615, heavy chain


Theoretical massNumber of molelcules
Total (without water)46,3112
Polymers46,3112
Non-polymers00
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-24 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.162, 84.474, 134.030
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 FAB ATN-615, light chain


Mass: 23269.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody FAB ATN-615, heavy chain


Mass: 23041.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.27 Å3/Da / Density % sol: 45.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 28%(w/v) PEG 3350, 100mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorDetector: CCD / Date: Oct 5, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.77→40.29 Å / Num. obs: 41141 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 24
Reflection shellResolution: 1.77→1.81 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2 / % possible all: 58.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→40.29 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 552172.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1953 5 %RANDOM
Rwork0.239 ---
obs0.239 39383 93.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.6582 Å2 / ksol: 0.345433 e/Å3
Displacement parametersBiso mean: 31.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20 Å2
2--1.56 Å20 Å2
3----2.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.77→40.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3261 0 0 178 3439
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d27.3
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it5.151.5
X-RAY DIFFRACTIONc_mcangle_it7.122
X-RAY DIFFRACTIONc_scbond_it6.872
X-RAY DIFFRACTIONc_scangle_it9.792.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 1.77→1.81 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.407 83 4.4 %
Rwork0.355 1812 -
obs--24.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2temp.dummy.param
X-RAY DIFFRACTION3carbohydrate.param
X-RAY DIFFRACTION4water_rep.param
X-RAY DIFFRACTION5ion.param

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