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- PDB-3wor: Crystal structure of the DAP BII octapeptide complex -

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Basic information

Entry
Database: PDB / ID: 3wor
TitleCrystal structure of the DAP BII octapeptide complex
Components
  • Angiotensin II
  • dipeptidyl aminopeptidase BII
KeywordsHydrolase/Hormone / Chymotrypsin fold / S46 peptidase / Hydrolase-Hormone complex
Function / homology
Function and homology information


regulation of blood volume by renin-angiotensin / response to muscle activity involved in regulation of muscle adaptation / type 2 angiotensin receptor binding / negative regulation of neurotrophin TRK receptor signaling pathway / regulation of renal sodium excretion / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / maintenance of blood vessel diameter homeostasis by renin-angiotensin / Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases / regulation of extracellular matrix assembly / regulation of renal output by angiotensin ...regulation of blood volume by renin-angiotensin / response to muscle activity involved in regulation of muscle adaptation / type 2 angiotensin receptor binding / negative regulation of neurotrophin TRK receptor signaling pathway / regulation of renal sodium excretion / G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger / maintenance of blood vessel diameter homeostasis by renin-angiotensin / Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases / regulation of extracellular matrix assembly / regulation of renal output by angiotensin / positive regulation of extracellular matrix assembly / renin-angiotensin regulation of aldosterone production / renal system process / serine-type aminopeptidase activity / vasoconstriction / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of cholesterol metabolic process / type 1 angiotensin receptor binding / response to angiotensin / low-density lipoprotein particle remodeling / positive regulation of macrophage derived foam cell differentiation / dipeptidyl-peptidase activity / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of cardiac muscle hypertrophy / negative regulation of MAP kinase activity / positive regulation of gap junction assembly / blood vessel remodeling / regulation of cardiac conduction / regulation of vasoconstriction / positive regulation of epithelial to mesenchymal transition / Metabolism of Angiotensinogen to Angiotensins / nitric oxide-cGMP-mediated signaling / positive regulation of endothelial cell migration / proteolysis involved in protein catabolic process / Peptide ligand-binding receptors / positive regulation of cytokine production / angiotensin-activated signaling pathway / growth factor activity / kidney development / regulation of cell growth / serine-type endopeptidase inhibitor activity / PPARA activates gene expression / hormone activity / positive regulation of miRNA transcription / regulation of blood pressure / positive regulation of reactive oxygen species metabolic process / positive regulation of fibroblast proliferation / positive regulation of inflammatory response / cell-cell signaling / regulation of cell population proliferation / : / regulation of apoptotic process / G alpha (i) signalling events / phospholipase C-activating G protein-coupled receptor signaling pathway / blood microparticle / G alpha (q) signalling events / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / G protein-coupled receptor signaling pathway / positive regulation of DNA-templated transcription / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Angiotensinogen, serpin domain / Angiotensinogen / Peptidase S46 / Peptidase S46 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily ...Angiotensinogen, serpin domain / Angiotensinogen / Peptidase S46 / Peptidase S46 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Angiotensinogen / Dipeptidyl aminopeptidase BII
Similarity search - Component
Biological speciesPseudoxanthomonas mexicana (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSakamoto, Y. / Suzuki, Y. / Iizuka, I. / Tateoka, C. / Roppongi, S. / Fujimoto, M. / Nonaka, T. / Ogasawara, W. / Tanaka, N.
CitationJournal: SCI REP / Year: 2014
Title: S46 peptidases are the first exopeptidases to be members of clan PA
Authors: Sakamoto, Y. / Suzuki, Y. / Iizuka, I. / Tateoka, C. / Roppongi, S. / Fujimoto, M. / Inaka, K. / Tanaka, H. / Masaki, M. / Ohta, K. / Okada, H. / Nonaka, T. / Morikawa, Y. / Nakamura, K.T. / ...Authors: Sakamoto, Y. / Suzuki, Y. / Iizuka, I. / Tateoka, C. / Roppongi, S. / Fujimoto, M. / Inaka, K. / Tanaka, H. / Masaki, M. / Ohta, K. / Okada, H. / Nonaka, T. / Morikawa, Y. / Nakamura, K.T. / Ogasawara, W. / Tanaka, N.
History
DepositionDec 29, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: dipeptidyl aminopeptidase BII
B: dipeptidyl aminopeptidase BII
C: Angiotensin II
D: Angiotensin II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,70917
Polymers154,6194
Non-polymers1,09013
Water18,5191028
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-111 kcal/mol
Surface area54540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.008, 122.008, 219.157
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1135-

HOH

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Components

#1: Protein dipeptidyl aminopeptidase BII / DAP BII


Mass: 76261.203 Da / Num. of mol.: 2 / Mutation: H86A, D224A, S657A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoxanthomonas mexicana (bacteria) / Strain: WO24 / Production host: Escherichia coli (E. coli)
References: UniProt: V5YM14, Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases
#2: Protein/peptide Angiotensin II


Mass: 1048.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P01019*PLUS
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1028 / 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: 2.56 Å3/Da / Density % sol: 51.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 18% PEG 8000, 20% Glycerol, 2mM ZnCl2, 80mM CHES, 2mM Angiotensin II, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 91253 / % possible obs: 100 %

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WOI

3woi


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.523 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22642 4807 5 %RANDOM
Rwork0.166 ---
obs0.16896 91253 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.767 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--0.3 Å20 Å2
3----0.6 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10836 0 58 1028 11922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01911121
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210582
X-RAY DIFFRACTIONr_angle_refined_deg1.8071.96115059
X-RAY DIFFRACTIONr_angle_other_deg0.8633.00124300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.07651402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.65424.336512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.485151814
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8591572
X-RAY DIFFRACTIONr_chiral_restr0.1050.21615
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02112810
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022554
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_it2.3372.7715620
X-RAY DIFFRACTIONr_mcbond_other2.3362.775619
X-RAY DIFFRACTIONr_mcangle_it3.2214.1477018
X-RAY DIFFRACTIONr_mcangle_other3.2214.1487019
X-RAY DIFFRACTIONr_scbond_it3.563.1915501
X-RAY DIFFRACTIONr_scbond_other3.5593.1915501
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4264.5988042
X-RAY DIFFRACTIONr_long_range_B_refined6.84323.37613799
X-RAY DIFFRACTIONr_long_range_B_other6.71923.05313349
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.104→2.158 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 314 -
Rwork0.213 6412 -
obs--96.57 %

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