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- PDB-2o3e: Crystal structure of engineered neurolysin with thimet oligopepti... -

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Basic information

Entry
Database: PDB / ID: 2o3e
TitleCrystal structure of engineered neurolysin with thimet oligopeptidase specificity for neurotensin cleavage site.
ComponentsNeurolysin
KeywordsHYDROLASE / thermolysin-like domain / substrate-binding channel
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 / metalloendopeptidase activity ...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 / metalloendopeptidase activity / mitochondrial intermembrane space / peptidase activity / mitochondrion / 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 family M3 / Peptidase M3A/M3B / 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 family M3 / Peptidase M3A/M3B / Neurolysin; domain 3 / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Neutral zinc metallopeptidases, zinc-binding region signature. / Up-down Bundle / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Neurolysin, mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Structure of neurolysin reveals a deep channel that limits substrate access.
Authors: Brown, C.K. / Madauss, K. / Lian, W. / Beck, M.R. / Tolbert, W.D. / Rodgers, D.W.
History
DepositionDec 1, 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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_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_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: Neurolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7102
Polymers77,6451
Non-polymers651
Water3,765209
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.550, 87.700, 58.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological unit is a single monomer.

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Components

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


Mass: 77644.641 Da / Num. of mol.: 1 / Mutation: R470E, T499R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Nln / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: P42676, neurolysin
#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


Mass: 18.015 Da / Num. of mol.: 209 / 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: 53.24 %
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: 0.997 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 2.2→43.85 Å / Num. obs: 42607 / % possible obs: 98.7 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.088 / Χ2: 1.278 / Net I/σ(I): 12.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.412 / Num. unique all: 4220 / Χ2: 1.222 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1refinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I1I

1i1i


Resolution: 2.2→43.85 Å / Rfactor Rfree error: 0.004 / FOM work R set: 0.812 / Data cutoff high absF: 2169754 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.268 4201 10.1 %RANDOM
Rwork0.219 ---
obs-41630 97.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.883 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso mean: 39.3 Å2
Baniso -1Baniso -2Baniso -3
1-6.4 Å20 Å20 Å2
2---0.37 Å20 Å2
3----6.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.2→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5351 0 1 209 5561
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.2
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.062
X-RAY DIFFRACTIONc_scbond_it2.222
X-RAY DIFFRACTIONc_scangle_it3.242.5
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
2.2-2.210.33910.264702793
2.21-2.230.278710.259743814
2.23-2.250.312820.26783865
2.25-2.260.365850.259680765
2.26-2.280.331720.265767839
2.28-2.30.339810.253727808
2.3-2.310.326940.262716810
2.31-2.330.256990.221740839
2.33-2.350.321940.261735829
2.35-2.370.293810.256715796
2.37-2.390.317800.258756836
2.39-2.410.351850.242717802
2.41-2.430.309600.236794854
2.43-2.450.244800.22749829
2.45-2.480.282750.233724799
2.48-2.50.309910.239745836
2.5-2.530.299670.241766833
2.53-2.550.287770.231726803
2.55-2.580.286850.235765850
2.58-2.610.326930.244716809
2.61-2.640.323900.261755845
2.64-2.670.294820.252748830
2.67-2.70.373740.24752826
2.7-2.740.265830.253724807
2.74-2.770.317980.237769867
2.77-2.810.331910.272736827
2.81-2.850.268940.227730824
2.85-2.890.296880.218738826
2.89-2.940.316780.256770848
2.94-2.990.305910.264719810
2.99-3.040.289750.244758833
3.04-3.090.355780.264772850
3.09-3.150.32810.264733814
3.15-3.220.328960.244745841
3.22-3.290.281940.25746840
3.29-3.360.277870.233738825
3.36-3.450.258760.237769845
3.45-3.540.28920.233752844
3.54-3.640.254630.216781844
3.64-3.760.259850.203733818
3.76-3.90.25810.19761842
3.9-4.050.225810.184754835
4.05-4.240.197770.188763840
4.24-4.460.227860.179745831
4.46-4.740.219860.172755841
4.74-5.10.1911030.17743846
5.1-5.620.301850.215778863
5.62-6.430.27910.254773864
6.43-8.090.2261040.203765869
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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