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- PDB-1i1i: NEUROLYSIN (ENDOPEPTIDASE 24.16) CRYSTAL STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1i1i
TitleNEUROLYSIN (ENDOPEPTIDASE 24.16) CRYSTAL STRUCTURE
ComponentsNEUROLYSIN
KeywordsHYDROLASE / neuropeptidase / zinc metallopeptidase / endopeptidase
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
Neurolysin, mitochondrial
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.3 Å
AuthorsBrown, C.K. / Madauss, K. / Lian, W. / Tolbert, W.D. / Beck, M.R. / Rodgers, D.W.
Citation
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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and Preliminary Analysis of Neurolysin
Authors: Lian, W. / Chen, G. / Wu, D. / Brown, C.K. / Madauss, K. / Hersh, L.B. / Rodgers, D.W.
History
DepositionFeb 1, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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

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Assembly

Deposited unit
P: NEUROLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0063
Polymers77,8751
Non-polymers1312
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
P: NEUROLYSIN
hetero molecules

P: NEUROLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,0116
Polymers155,7502
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area1420 Å2
ΔGint-152 kcal/mol
Surface area57910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.6, 87.7, 58.3
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein NEUROLYSIN /


Mass: 77874.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: PBADC / 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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.6 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, cacodylate, magnesium chloride, zinc chloride, 2-mercaptoethanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
Conc.: 0.2 mM / Chemical formula: MeHgCl

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Data collection

DiffractionMean temperature: 108 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 12, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 36511 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 23.9
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 7.8 / % possible all: 95.5
Reflection shell
*PLUS
% possible obs: 95.5 %

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.268 3644 RANDOM
Rwork0.224 --
all-36511 -
obs-36511 -
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5348 0 2 172 5522
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_dihedral_angle_d20.5
X-RAY DIFFRACTIONc_improper_angle_d0.8
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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