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- PDB-1jjo: Crystal Structure of Mouse Neuroserpin (Cleaved form) -

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Basic information

Entry
Database: PDB / ID: 1jjo
TitleCrystal Structure of Mouse Neuroserpin (Cleaved form)
Components(NEUROSERPIN) x 3
KeywordsSIGNALING PROTEIN / Serpin / Serine protease inhibitor / Neuronal serpin
Function / homology
Function and homology information


cytoplasmic vesicle lumen / negative regulation of endopeptidase activity / regulation of cell adhesion / serine-type endopeptidase inhibitor activity / positive regulation of neuron projection development / perikaryon / secretory granule lumen / neuronal cell body / extracellular space
Similarity search - Function
Helix hairpin bin / Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain ...Helix hairpin bin / Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Helix Hairpins / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.06 Å
AuthorsBriand, C. / Kozlov, S.V. / Sonderegger, P. / Gruetter, M.G.
CitationJournal: FEBS Lett. / Year: 2001
Title: Crystal structure of neuroserpin: a neuronal serpin involved in a conformational disease.
Authors: Briand, C. / Kozlov, S.V. / Sonderegger, P. / Grutter, M.G.
History
DepositionJul 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEUROSERPIN
C: NEUROSERPIN
E: NEUROSERPIN
B: NEUROSERPIN
D: NEUROSERPIN
F: NEUROSERPIN


Theoretical massNumber of molelcules
Total (without water)76,0326
Polymers76,0326
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17790 Å2
ΔGint-153 kcal/mol
Surface area26170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.290, 108.690, 45.990
Angle α, β, γ (deg.)90.00, 101.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide NEUROSERPIN / PROTEASE INHIBITOR 17


Mass: 4416.040 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: SERPINI1 or PI12 or SPI17 / Plasmid: PAK400 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: O35684
#2: Protein NEUROSERPIN / PROTEASE INHIBITOR 17


Mass: 29630.404 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: SERPINI1 or PI12 or SPI17 / Plasmid: PAK400 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: O35684
#3: Protein/peptide NEUROSERPIN / PROTEASE INHIBITOR 17


Mass: 3969.749 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: SERPINI1 or PI12 or SPI17 / Plasmid: PAK400 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: O35684

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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: 2.07 Å3/Da / Density % sol: 40.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 25% PEG8000, 0.2M H2PO4(NH4), 0.1M Tris-HCl, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
125 mg/mlprotein1drop
225 %PEG80001reservoir
30.2 M1reservoirH2PO4(NH4)
40.1 MTris-HCl1reservoirpH6.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 6, 1999
RadiationMonochromator: mirror, Prophysics XRM-216 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.06→16.86 Å / Num. all: 11124 / Num. obs: 9419 / % possible obs: 79.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 2.57 % / Rsym value: 0.155 / Net I/σ(I): 7
Reflection shellResolution: 3.06→3.1 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2 / Num. unique all: 417 / Rsym value: 0.421 / % possible all: 94.6
Reflection
*PLUS
Lowest resolution: 17 Å / Rmerge(I) obs: 0.155
Reflection shell
*PLUS
% possible obs: 74.6 % / Num. unique obs: 7975 / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology model based on all available cleaved serpin structures

Resolution: 3.06→16.89 Å / Isotropic thermal model: anisotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Bulk solvent correction, strict NCS
RfactorNum. reflection% reflectionSelection details
Rfree0.308 505 -Random
Rwork0.232 ---
all-11124 --
obs-9419 79.7 %-
Refinement stepCycle: LAST / Resolution: 3.06→16.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5074 0 0 0 5074
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.41895
X-RAY DIFFRACTIONc_bond_d0.008035
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4.3 % / Rfactor obs: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS

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