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- PDB-2z3z: Prolyl tripeptidyl aminopeptidase mutant E636A complexd with an i... -

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Basic information

Entry
Database: PDB / ID: 2z3z
TitleProlyl tripeptidyl aminopeptidase mutant E636A complexd with an inhibitor
ComponentsDipeptidyl aminopeptidase IV
KeywordsHYDROLASE / peptidase family S9 / prolyl oligopeptidase family / serine protease / proline-specific peptidase
Function / homology
Function and homology information


Xaa-Xaa-Pro tripeptidyl-peptidase / aminopeptidase activity / serine-type peptidase activity / proteolysis
Similarity search - Function
Dipeptidylpeptidase IV, N-terminal domain / 8 Propeller / Methanol Dehydrogenase; Chain A / : / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold ...Dipeptidylpeptidase IV, N-terminal domain / 8 Propeller / Methanol Dehydrogenase; Chain A / : / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-AIO / Prolyl tripeptidyl peptidase
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.95 Å
AuthorsXu, Y. / Nakajima, Y. / Ito, K. / Yoshimoto, T.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Novel inhibitor for prolyl tripeptidyl aminopeptidase from Porphyromonas gingivalis and details of substrate-recognition mechanism
Authors: Xu, Y. / Nakajima, Y. / Ito, K. / Zheng, H. / Oyama, H. / Heiser, U. / Hoffmann, T. / Gartner, U.T. / Demuth, H.U. / Yoshimoto, T.
History
DepositionJun 9, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 23, 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: Dipeptidyl aminopeptidase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9423
Polymers79,5471
Non-polymers3952
Water10,881604
1
A: Dipeptidyl aminopeptidase IV
hetero molecules

A: Dipeptidyl aminopeptidase IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,8846
Polymers159,0932
Non-polymers7904
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_556-x,-x+y,-z+11
Buried area5970 Å2
ΔGint-35 kcal/mol
Surface area51600 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)149.825, 149.825, 161.506
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Dipeptidyl aminopeptidase IV / prolyl tripeptidyl aminopeptidase


Mass: 79546.742 Da / Num. of mol.: 1 / Fragment: residues 39-732 / Mutation: E636A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: PG1316 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: Q7MUW6, Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-AIO / [(2R)-1-(L-ALANYL-L-ISOLEUCYL)PYRROLIDIN-2-YL]BORONIC ACID


Mass: 299.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H26BN3O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / 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: 3.29 Å3/Da / Density % sol: 62.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1.1M pottasium sodium tartrate, 0.2M lithium sulfate, 0.1M CHES buffer, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 4, 2006 / Details: monochrometor
RadiationMonochromator: Si(111) double crystal monochromertor / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 77814 / Num. obs: 77814 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 83.8
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 18.7 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 11 / Num. unique all: 7590 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2Z3W

2z3w


Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.59 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.127 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21188 3765 5 %RANDOM
Rwork0.18273 ---
obs0.18419 71475 96.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.539 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å2-0.2 Å20 Å2
2---0.4 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5161 0 26 604 5791
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225328
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3861.9467242
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3685646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.19623.2250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8615829
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3581534
X-RAY DIFFRACTIONr_chiral_restr0.1030.2776
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024121
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.22384
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.23601
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2579
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9221.53314
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4625194
X-RAY DIFFRACTIONr_scbond_it2.26532338
X-RAY DIFFRACTIONr_scangle_it3.4154.52048
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 245 -
Rwork0.217 5255 -
obs--97.74 %

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