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- PDB-6vgr: Crystal Structure of Human Dipeptidase 3 in Complex with Fab of SC-003 -

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Basic information

Entry
Database: PDB / ID: 6vgr
TitleCrystal Structure of Human Dipeptidase 3 in Complex with Fab of SC-003
Components
  • Dipeptidase 3
  • SC-003 Fab Heavy Chain
  • SC-003 Fab Light Chain
KeywordsHYDROLASE / Fab / Antibody Drug Conjugate / Dipeptidase
Function / homology
Function and homology information


LTC4-CYSLTR mediated IL4 production / Aflatoxin activation and detoxification / Synthesis of Leukotrienes (LT) and Eoxins (EX) / dipeptidase activity / acrosomal vesicle / proteolysis / membrane / plasma membrane
Similarity search - Function
Dipeptidase 2/3 / Membrane dipeptidase, active site / Renal dipeptidase active site. / Peptidase M19 / Membrane dipeptidase (Peptidase family M19) / Renal dipeptidase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsHayashi, K. / Longenecker, K.L. / Vivona, S.
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Structure of human DPEP3 in complex with the SC-003 antibody Fab fragment reveals basis for lack of dipeptidase activity.
Authors: Hayashi, K. / Longenecker, K.L. / Koenig, P. / Prashar, A. / Hampl, J. / Stoll, V. / Vivona, S.
History
DepositionJan 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Dipeptidase 3
B: Dipeptidase 3
C: SC-003 Fab Heavy Chain
D: SC-003 Fab Light Chain
H: SC-003 Fab Heavy Chain
L: SC-003 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)203,2876
Polymers203,2876
Non-polymers00
Water3,639202
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13210 Å2
ΔGint-53 kcal/mol
Surface area60870 Å2
Unit cell
Length a, b, c (Å)167.030, 167.030, 116.380
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Dipeptidase 3


Mass: 53745.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPEP3, UNQ834/PRO1772 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q9H4B8, membrane dipeptidase
#2: Antibody SC-003 Fab Heavy Chain


Mass: 24213.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody SC-003 Fab Light Chain


Mass: 23684.293 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O

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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: 2.31 Å3/Da / Density % sol: 46.65 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 0.1 M calcium acetate, 0.1 M sodium acetate pH 4.5, 10% w/v PEG4000

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Data collection

DiffractionMean temperature: 297 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.84→40.12 Å / Num. obs: 42049 / % possible obs: 96.2 % / Redundancy: 10.2 % / Rrim(I) all: 0.091 / Net I/σ(I): 20
Reflection shellResolution: 2.84→2.89 Å / Num. unique obs: 2173 / Rpim(I) all: 0.356

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VGO

6vgo


Resolution: 2.84→40.12 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.904 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.372
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2073 4.93 %RANDOM
Rwork0.19 ---
obs0.193 42033 96.2 %-
Displacement parametersBiso max: 197.24 Å2 / Biso mean: 80.94 Å2 / Biso min: 31.61 Å2
Baniso -1Baniso -2Baniso -3
1--12.853 Å20 Å20 Å2
2---12.853 Å20 Å2
3---25.7059 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: final / Resolution: 2.84→40.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12070 0 0 202 12272
Biso mean---63.05 -
Num. residues----1562
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4188SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2088HARMONIC5
X-RAY DIFFRACTIONt_it12338HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1598SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14278SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d12338HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg16768HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion3.45
X-RAY DIFFRACTIONt_other_torsion19.55
LS refinement shellResolution: 2.84→2.86 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.4085 46 5.47 %
Rwork0.2381 795 -
all0.247 841 -
obs--100 %

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