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- PDB-6vgo: Crystal Structure of Human Dipeptidase 3 -

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Basic information

Entry
Database: PDB / ID: 6vgo
TitleCrystal Structure of Human Dipeptidase 3
ComponentsDipeptidase 3
KeywordsHYDROLASE / Metalloprotease
Function / homology
Function and homology information


dipeptidase activity / side of membrane / acrosomal vesicle / proteolysis / membrane / plasma membrane
Similarity search - Function
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: 1.82 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dipeptidase 3


Theoretical massNumber of molelcules
Total (without water)53,7451
Polymers53,7451
Non-polymers00
Water3,963220
1
A: Dipeptidase 3

A: Dipeptidase 3


Theoretical massNumber of molelcules
Total (without water)107,4902
Polymers107,4902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area2230 Å2
ΔGint-8 kcal/mol
Surface area25130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.880, 65.880, 194.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Dipeptidase 3


Mass: 53745.145 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 1.96 Å3/Da / Density % sol: 37.29 %
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: Dec 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→62.39 Å / Num. obs: 39548 / % possible obs: 99.8 % / Redundancy: 12.7 % / Rrim(I) all: 0.078 / Net I/σ(I): 18
Reflection shellResolution: 1.82→1.85 Å / Num. unique obs: 1939 / Rpim(I) all: 0.38

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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: 1ITQ

1itq


Resolution: 1.82→62.39 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.117 / SU Rfree Blow DPI: 0.11 / SU Rfree Cruickshank DPI: 0.106
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1997 5.05 %RANDOM
Rwork0.186 ---
obs0.187 39548 99.8 %-
Displacement parametersBiso max: 116.41 Å2 / Biso mean: 39.11 Å2 / Biso min: 24.14 Å2
Baniso -1Baniso -2Baniso -3
1--5.2057 Å20 Å20 Å2
2---5.2057 Å20 Å2
3---10.4115 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: final / Resolution: 1.82→62.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2732 0 0 220 2952
Biso mean---48.56 -
Num. residues----350
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d987SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes480HARMONIC5
X-RAY DIFFRACTIONt_it2779HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion353SEMIHARMONIC5
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_contact3512SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2779HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3764HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion3.59
X-RAY DIFFRACTIONt_other_torsion14.98
LS refinement shellResolution: 1.82→1.83 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2279 52 6.57 %
Rwork0.2264 739 -
all0.2265 791 -
obs--99.36 %

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