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- PDB-4fxy: Crystal structure of rat neurolysin with bound pyrazolidin inhibitor -

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Basic information

Entry
Database: PDB / ID: 4fxy
TitleCrystal structure of rat neurolysin with bound pyrazolidin inhibitor
ComponentsNeurolysin, mitochondrial
KeywordsHYDROLASE/HYDROLASE INHIBITOR / hydrolase / endopeptidase / zinc metallopeptidase / neuropeptidase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


neurolysin / regulation of skeletal muscle fiber differentiation / Peptide ligand-binding receptors / oligopeptidase activity / peptide metabolic process / regulation of gluconeogenesis / peptide catabolic process / peptide binding / protein catabolic process / mitochondrial intermembrane space ...neurolysin / regulation of skeletal muscle fiber differentiation / Peptide ligand-binding receptors / oligopeptidase activity / peptide metabolic process / regulation of gluconeogenesis / peptide catabolic process / peptide binding / protein catabolic process / mitochondrial intermembrane space / metalloendopeptidase activity / peptidase activity / proteolysis / metal ion binding / plasma membrane / 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
Chem-0W2 / Neurolysin, mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRodgers, D.W. / Hines, C.S.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Allosteric inhibition of the neuropeptidase neurolysin.
Authors: Hines, C.S. / Ray, K. / Schmidt, J.J. / Xiong, F. / Feenstra, R.W. / Pras-Raves, M. / de Moes, J.P. / Lange, J.H. / Melikishvili, M. / Fried, M.G. / Mortenson, P. / Charlton, M. / Patel, Y. ...Authors: Hines, C.S. / Ray, K. / Schmidt, J.J. / Xiong, F. / Feenstra, R.W. / Pras-Raves, M. / de Moes, J.P. / Lange, J.H. / Melikishvili, M. / Fried, M.G. / Mortenson, P. / Charlton, M. / Patel, Y. / Courtney, S.M. / Kruse, C.G. / Rodgers, D.W.
History
DepositionJul 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Other
Revision 1.2Nov 19, 2014Group: Database references
Revision 1.3Jan 14, 2015Group: Database references
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Sep 13, 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.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_label_asym_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
P: Neurolysin, mitochondrial
Q: Neurolysin, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,9366
Polymers158,7552
Non-polymers1,1814
Water4,630257
1
P: Neurolysin, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9683
Polymers79,3781
Non-polymers5902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
Q: Neurolysin, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9683
Polymers79,3781
Non-polymers5902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.000, 131.400, 144.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Neurolysin, mitochondrial / / Microsomal endopeptidase / MEP / Mitochondrial oligopeptidase M / Neurotensin endopeptidase


Mass: 79377.648 Da / Num. of mol.: 2 / Mutation: H160A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nln / Plasmid: pBAD/His C / Production host: Escherichia coli (E. coli) / Strain (production host): TOP 10 / References: UniProt: P42676, neurolysin
#2: Chemical ChemComp-0W2 / 1-{(2S)-1-[(3R)-3-(2-chlorophenyl)-2-(2-fluorophenyl)pyrazolidin-1-yl]-1-oxopropan-2-yl}-3-[(1R,3S,5R,7R)-tricyclo[3.3.1.1~3,7~]dec-2-yl]urea


Mass: 525.057 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H34ClFN4O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.63 Å3/Da / Density % sol: 53.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES, pH, 7.0, 0.1 M LiSO4, 2 mM -mercaptoethanol and 12-15% polyethylene glycol 4000., VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: SBC-2 / Detector: CCD / Date: Jan 1, 2003
RadiationMonochromator: double crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 43793 / Num. obs: 43760 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rsym value: 0.162 / Net I/σ(I): 8.8
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3.1 / Rsym value: 0.44 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.2_869)refinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1I1I

1i1i


Resolution: 2.8→48.654 Å / SU ML: 0.28 / Isotropic thermal model: isotropic / σ(F): 1.34 / Phase error: 32.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2871 4180 9.98 %
Rwork0.2349 --
obs0.2403 41891 99.57 %
all-41894 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.9154 Å2-0 Å20 Å2
2---5.4487 Å2-0 Å2
3---9.3284 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10670 0 76 257 11003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00510972
X-RAY DIFFRACTIONf_angle_d0.80714698
X-RAY DIFFRACTIONf_dihedral_angle_d19.0384112
X-RAY DIFFRACTIONf_chiral_restr0.0551620
X-RAY DIFFRACTIONf_plane_restr0.0041894
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.83180.35081390.29551261X-RAY DIFFRACTION100
2.8318-2.86510.38231190.29941236X-RAY DIFFRACTION99
2.8651-2.90010.38721400.30111235X-RAY DIFFRACTION100
2.9001-2.93680.30671320.29571250X-RAY DIFFRACTION99
2.9368-2.97540.32191440.29861231X-RAY DIFFRACTION100
2.9754-3.01620.40191410.29661234X-RAY DIFFRACTION99
3.0162-3.05920.34231480.30141242X-RAY DIFFRACTION100
3.0592-3.10490.30351270.28421247X-RAY DIFFRACTION100
3.1049-3.15340.37211310.29641252X-RAY DIFFRACTION99
3.1534-3.20510.31671360.27561233X-RAY DIFFRACTION100
3.2051-3.26040.33191430.27981243X-RAY DIFFRACTION100
3.2604-3.31960.3141510.26191210X-RAY DIFFRACTION99
3.3196-3.38350.31251480.26351266X-RAY DIFFRACTION100
3.3835-3.45250.30411390.25421246X-RAY DIFFRACTION100
3.4525-3.52760.32251490.24921236X-RAY DIFFRACTION100
3.5276-3.60960.26241320.22731251X-RAY DIFFRACTION100
3.6096-3.69980.31481300.22661269X-RAY DIFFRACTION100
3.6998-3.79980.25391290.21861247X-RAY DIFFRACTION100
3.7998-3.91160.28541210.21291278X-RAY DIFFRACTION100
3.9116-4.03780.29211390.2091268X-RAY DIFFRACTION100
4.0378-4.1820.23131520.20291238X-RAY DIFFRACTION100
4.182-4.34940.27831450.20321248X-RAY DIFFRACTION100
4.3494-4.54720.2411430.18771274X-RAY DIFFRACTION100
4.5472-4.78670.24421290.17851263X-RAY DIFFRACTION100
4.7867-5.08630.23551450.1841264X-RAY DIFFRACTION100
5.0863-5.47860.25981560.21231289X-RAY DIFFRACTION100
5.4786-6.0290.26731360.21221271X-RAY DIFFRACTION100
6.029-6.89930.30861340.221313X-RAY DIFFRACTION99
6.8993-8.68430.22581460.19981299X-RAY DIFFRACTION100
8.6843-48.66090.18981560.19381317X-RAY DIFFRACTION96

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