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- PDB-2o36: Crystal structure of engineered thimet oligopeptidase with neurol... -

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Basic information

Entry
Database: PDB / ID: 2o36
TitleCrystal structure of engineered thimet oligopeptidase with neurolysin specificity in neurotensin cleavage site
ComponentsThimet oligopeptidase
KeywordsHYDROLASE / thermolysin-like domain / substrate-binding channel
Function / homology
Function and homology information


thimet oligopeptidase / peptide metabolic process / mitochondrial intermembrane space / metalloendopeptidase activity / protein polyubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / proteolysis / metal ion binding / cytosol
Similarity search - Function
Neurolysin, domain 3 / Endopeptidase. Chain P; domain 1 / Neurolysin/Thimet oligopeptidase, N-terminal / Neurolysin/Thimet oligopeptidase, domain 2 / Peptidase M3A/M3B catalytic domain / Peptidase M3A/M3B / Peptidase family M3 / Neurolysin; domain 3 / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) ...Neurolysin, domain 3 / Endopeptidase. Chain P; domain 1 / Neurolysin/Thimet oligopeptidase, N-terminal / Neurolysin/Thimet oligopeptidase, domain 2 / Peptidase M3A/M3B catalytic domain / Peptidase M3A/M3B / Peptidase family M3 / Neurolysin; domain 3 / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Up-down Bundle / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Thimet oligopeptidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsRodgers, D.W. / Lim, E.J.
Citation
Journal: J.Biol.Chem. / Year: 2007
Title: Swapping the substrate specificities of the neuropeptidases neurolysin and thimet oligopeptidase.
Authors: Lim, E.J. / Sampath, S. / Coll-Rodriguez, J. / Schmidt, J. / Ray, K. / Rodgers, D.W.
#1: Journal: J.Biol.Chem. / Year: 2004
Title: Crystal structure of human thimet oligopeptidase provides insight into substrate recognition, regulation, and localization
Authors: Ray, K. / Hines, C.S. / Coll-Rodriguez, J. / Rodgers, D.W.
History
DepositionNov 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_label_seq_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 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thimet oligopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,5472
Polymers77,4821
Non-polymers651
Water8,485471
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.120, 99.250, 105.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a single monomer

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Components

#1: Protein Thimet oligopeptidase / / Endopeptidase 24.15 / MP78


Mass: 77481.953 Da / Num. of mol.: 1 / Mutation: E469R, R498T, C246S, C253S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THOP1 / Plasmid: BL21(DE3)RP / Production host: Escherichia coli (E. coli) / References: UniProt: P52888, thimet oligopeptidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.65 Å3/Da / Density % sol: 53.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9997 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9997 Å / Relative weight: 1
ReflectionResolution: 1.94→30 Å / Num. obs: 59434 / % possible obs: 98.2 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.075 / Χ2: 1.075 / Net I/σ(I): 11
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.299 / Num. unique all: 5416 / Χ2: 0.923 / % possible all: 90.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S4B

1s4b


Resolution: 1.95→29.72 Å / Rfactor Rfree error: 0.003 / FOM work R set: 0.848 / Data cutoff high absF: 2315410.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 6023 10.1 %RANDOM
Rwork0.202 ---
obs-59387 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.842 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso mean: 25.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.3 Å20 Å20 Å2
2--2.38 Å20 Å2
3---1.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→29.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5302 0 1 471 5774
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d19.4
X-RAY DIFFRACTIONc_improper_angle_d0.73
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.94-1.950.25540.26462516
1.95-1.970.2841120.22710361148
1.97-1.980.3171100.24110841194
1.98-1.990.2741330.23310221155
1.99-2.010.2571390.22610391178
2.01-2.020.2981210.22110491170
2.02-2.040.2481180.21510561174
2.04-2.060.2571330.21410601193
2.06-2.070.2461150.19710521167
2.07-2.090.2811290.22210481177
2.09-2.110.2311240.20310731197
2.11-2.130.2551210.20410351156
2.13-2.140.2481080.19910891197
2.14-2.160.2551120.19410691181
2.16-2.180.2391380.19810401178
2.18-2.210.2421100.20210951205
2.21-2.230.2591260.20810291155
2.23-2.250.251160.19810951211
2.25-2.280.2271280.19510681196
2.28-2.30.2381300.19210231153
2.3-2.330.241060.1910981204
2.33-2.350.2631120.19510641176
2.35-2.380.2591070.19510971204
2.38-2.410.2251280.19610771205
2.41-2.440.2481140.20110541168
2.44-2.480.2581100.19510981208
2.48-2.510.2561120.20110731185
2.51-2.550.2441190.20110811200
2.55-2.590.2521280.21510711199
2.59-2.630.261230.21410731196
2.63-2.680.2711210.22110971218
2.68-2.730.2311190.20710681187
2.73-2.780.2771250.21410871212
2.78-2.840.2711250.22510721197
2.84-2.90.2731180.22110751193
2.9-2.970.2421200.21411081228
2.97-3.040.2711240.21910721196
3.04-3.120.2791140.21910871201
3.12-3.210.2721210.22811201241
3.21-3.320.2591100.21210921202
3.32-3.440.2171510.20410561207
3.44-3.570.2461110.20211091220
3.57-3.740.1931220.19311171239
3.74-3.930.21190.18711011220
3.93-4.180.1821490.16910841233
4.18-4.50.1711250.17711251250
4.5-4.950.2071230.17511161239
4.95-5.670.2511290.21911241253
5.67-7.140.2931310.23911481279
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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