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- PDB-1npm: NEUROPSIN, A SERINE PROTEASE EXPRESSED IN THE LIMBIC SYSTEM OF MO... -

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Basic information

Entry
Database: PDB / ID: 1npm
TitleNEUROPSIN, A SERINE PROTEASE EXPRESSED IN THE LIMBIC SYSTEM OF MOUSE BRAIN
ComponentsNEUROPSIN
KeywordsSERINE PROTEINASE / GLYCOPROTEIN
Function / homology
Function and homology information


Formation of the cornified envelope / kallikrein 8 / regulation of synapse organization / keratinocyte proliferation / serine protease inhibitor complex / neuron projection morphogenesis / secretory granule / synapse organization / memory / response to wounding ...Formation of the cornified envelope / kallikrein 8 / regulation of synapse organization / keratinocyte proliferation / serine protease inhibitor complex / neuron projection morphogenesis / secretory granule / synapse organization / memory / response to wounding / peptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / cytoplasm
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKishi, T. / Kato, M. / Shimizu, T. / Kato, K. / Matsumoto, K. / Yoshida, S. / Shiosaka, S. / Hakoshima, T.
Citation
Journal: J.Biol.Chem. / Year: 1999
Title: Crystal structure of neuropsin, a hippocampal protease involved in kindling epileptogenesis.
Authors: Kishi, T. / Kato, M. / Shimizu, T. / Kato, K. / Matsumoto, K. / Yoshida, S. / Shiosaka, S. / Hakoshima, T.
#1: Journal: J.Struct.Biol. / Year: 1997
Title: Crystallization and Preliminary X-Ray Analysis of Neuropsin, a Serine Protease Expressed in the Limbic System of Mouse Brain
Authors: Kishi, T. / Kato, M. / Shimizu, T. / Kato, K. / Matsumoto, K. / Yoshida, S. / Shiosaka, S. / Hakoshima, T.
History
DepositionJan 7, 1998Processing site: BNL
Revision 1.0Mar 23, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 9, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NEUROPSIN
B: NEUROPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8514
Polymers49,4082
Non-polymers4422
Water3,495194
1
A: NEUROPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9252
Polymers24,7041
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NEUROPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9252
Polymers24,7041
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.400, 55.160, 65.370
Angle α, β, γ (deg.)95.38, 89.98, 110.46
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (1, -0.00042, 0.00043), (-0.00042, -1, -0.00032), (0.00043, 0.00032, -1)
Vector: 19.06308, 14.01756, 35.32339)

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Components

#1: Protein NEUROPSIN


Mass: 24704.045 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: HIGH5 / Organ: HIPPOCAMPUS / Plasmid: PVL1392 / Cell line (production host): HIGH5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q61955
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 51 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
124.5 mg/mlprotein1drop
25 mMHEPES1reservoir
3100 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1
DetectorDetector: IMAGE PLATE / Date: Nov 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 2.1 Å / Num. obs: 24944 / % possible obs: 90 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.5
Reflection shellResolution: 2.1→2.24 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 3.1 / % possible all: 74.5
Reflection
*PLUS
% possible obs: 90.7 %
Reflection shell
*PLUS
% possible obs: 74.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALA(CCP4)data reduction
X-PLOR3.851model building
X-PLOR3.851refinement
CCP4(SCALA)data scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4PTP

4ptp
PDB Unreleased entry


Resolution: 2.1→100 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1267 4.9 %RANDOM
Rwork0.186 ---
obs0.186 25778 90.7 %-
Displacement parametersBiso mean: 31.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.1→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3408 0 28 194 3630
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.494
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.06
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.391
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.1→2.2 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.339 135 5 %
Rwork0.281 2533 -
obs--74.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM3.CHOTOPH19.SOL
X-RAY DIFFRACTION3TOPH3.CHO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.535
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_improper_angle_d
LS refinement shell
*PLUS
Rfactor obs: 0.281

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