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- PDB-4dvb: The crystal structure of the Fab fragment of pro-uPA antibody mAb-112 -

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Basic information

Entry
Database: PDB / ID: 4dvb
TitleThe crystal structure of the Fab fragment of pro-uPA antibody mAb-112
Components(Fab fragment of pro-uPA antibody mAb-112) x 2
KeywordsIMMUNE SYSTEM / HYDROLASE
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.93 Å
AuthorsJiang, L. / Botkjaer, K.A. / Andersen, L.M. / Yuan, C. / Andreasen, P.A. / Huang, M.
CitationJournal: Biochem.J. / Year: 2013
Title: Rezymogenation of active urokinase induced by an inhibitory antibody.
Authors: Jiang, L. / Botkjaer, K.A. / Andersen, L.M. / Yuan, C. / Andreasen, P.A. / Huang, M.
History
DepositionFeb 23, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab fragment of pro-uPA antibody mAb-112
B: Fab fragment of pro-uPA antibody mAb-112
H: Fab fragment of pro-uPA antibody mAb-112
L: Fab fragment of pro-uPA antibody mAb-112
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,07412
Polymers93,2084
Non-polymers8678
Water10,413578
1
A: Fab fragment of pro-uPA antibody mAb-112
B: Fab fragment of pro-uPA antibody mAb-112
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8925
Polymers46,6042
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-63 kcal/mol
Surface area20150 Å2
MethodPISA
2
H: Fab fragment of pro-uPA antibody mAb-112
L: Fab fragment of pro-uPA antibody mAb-112
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1827
Polymers46,6042
Non-polymers5785
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-41 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.177, 86.628, 155.331
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 fragment of pro-uPA antibody mAb-112


Mass: 23003.910 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Fab fragment of pro-uPA antibody mAb-112


Mass: 23599.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 578 / 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: 2.57 Å3/Da / Density % sol: 52.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 2.3M ammonium sulfate, 100mM Tris-HCl (pH 7.4), 5% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→77.67 Å / Num. obs: 67906 / % possible obs: 98.52 % / Redundancy: 9.9 %
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 7.4 % / % possible all: 95.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.93→77.67 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.927 / SU B: 3.988 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25899 3598 5 %RANDOM
Rwork0.22258 ---
obs0.22439 67906 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.998 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å20 Å2
2--2.02 Å20 Å2
3----1.49 Å2
Refinement stepCycle: LAST / Resolution: 1.93→77.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6524 0 48 578 7150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226729
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1361.9539157
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9455848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.38723.701254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83151074
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1661530
X-RAY DIFFRACTIONr_chiral_restr0.0810.21025
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214998
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4391.54249
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.86526892
X-RAY DIFFRACTIONr_scbond_it1.27432480
X-RAY DIFFRACTIONr_scangle_it2.1454.52265
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.933→1.983 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 287 -
Rwork0.265 4748 -
obs--96.22 %

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