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- PDB-3woq: Crystal structure of the DAP BII hexapeptide complex III -

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Basic information

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


Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases / serine-type aminopeptidase activity / dipeptidyl-peptidase activity / proteolysis involved in protein catabolic process / protein homodimerization activity / identical protein binding
Similarity search - Function
Peptidase S46 / Peptidase S46 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Dipeptidyl aminopeptidase BII
Similarity search - Component
Biological speciesPseudoxanthomonas mexicana (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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

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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 IV
D: Angiotensin IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,16517
Polymers154,0744
Non-polymers1,09013
Water13,962775
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-121 kcal/mol
Surface area53960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.700, 121.700, 218.809
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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 IV


Mass: 775.913 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Homo sapiens (human)
#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.: 775 / 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: 2.55 Å3/Da / Density % sol: 51.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 18% PEG 8000, 20% Glycerol, 2mM ZnCl2, 80mM CHES, 2mM Angiotensin IV, 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-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jan 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.82→40 Å / Num. obs: 138595 / % possible obs: 99.4 %

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Processing

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

3woi


Resolution: 1.82→39.92 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.772 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.227 7299 5 %RANDOM
Rwork0.18524 ---
obs0.1873 138595 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.943 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2--0.25 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.82→39.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10834 0 58 775 11667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01911123
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210580
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.96215065
X-RAY DIFFRACTIONr_angle_other_deg0.9013.00124300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43851402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.87624.353510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.378151808
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4431570
X-RAY DIFFRACTIONr_chiral_restr0.1150.21615
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02112808
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_it2.2392.4655620
X-RAY DIFFRACTIONr_mcbond_other2.2392.4655619
X-RAY DIFFRACTIONr_mcangle_it2.953.697018
X-RAY DIFFRACTIONr_mcangle_other2.9493.697019
X-RAY DIFFRACTIONr_scbond_it3.0172.7885503
X-RAY DIFFRACTIONr_scbond_other3.0132.7885503
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5024.0348048
X-RAY DIFFRACTIONr_long_range_B_refined5.57320.3413463
X-RAY DIFFRACTIONr_long_range_B_other5.50820.21713153
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 513 -
Rwork0.24 9636 -
obs--94.36 %

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