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- PDB-6h8m: Crystal structure of the third SRCR domain of Murine Neurotrypsin. -

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Basic information

Entry
Database: PDB / ID: 6h8m
TitleCrystal structure of the third SRCR domain of Murine Neurotrypsin.
ComponentsNeurotrypsin
KeywordsHYDROLASE / Neurotrypsin / Extracellular protease / SRCR domain / CRD domain
Function / homology
Function and homology information


scavenger receptor activity / zymogen activation / exocytosis / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / synaptic cleft / terminal bouton / peptidase activity / cytoplasmic vesicle / axon / serine-type endopeptidase activity ...scavenger receptor activity / zymogen activation / exocytosis / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / synaptic cleft / terminal bouton / peptidase activity / cytoplasmic vesicle / axon / serine-type endopeptidase activity / synapse / dendrite / proteolysis / plasma membrane
Similarity search - Function
Mac-2 Binding Protein / SRCR-like domain / SRCR domain signature. / Scavenger receptor cysteine-rich domain / SRCR domain / SRCR domain profile. / SRCR-like domain / SRCR-like domain superfamily / Scavenger receptor Cys-rich / Kringle domain ...Mac-2 Binding Protein / SRCR-like domain / SRCR domain signature. / Scavenger receptor cysteine-rich domain / SRCR domain / SRCR domain profile. / SRCR-like domain / SRCR-like domain superfamily / Scavenger receptor Cys-rich / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / 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 domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Roll / Peptidase S1, PA clan / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCanciani, A. / Forneris, F.
CitationJournal: Protein Sci. / Year: 2019
Title: Structural characterization of the third scavenger receptor cysteine-rich domain of murine neurotrypsin.
Authors: Canciani, A. / Catucci, G. / Forneris, F.
History
DepositionAug 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neurotrypsin
B: Neurotrypsin


Theoretical massNumber of molelcules
Total (without water)25,0122
Polymers25,0122
Non-polymers00
Water1,53185
1
A: Neurotrypsin


Theoretical massNumber of molelcules
Total (without water)12,5061
Polymers12,5061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neurotrypsin


Theoretical massNumber of molelcules
Total (without water)12,5061
Polymers12,5061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.752, 62.902, 84.526
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 107
2010B1 - 107

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Components

#1: Protein Neurotrypsin / Brain-specific serine protease 3 / BSSP-3 / Motopsin / Serine protease 12


Mass: 12506.126 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The first two residues of the provided sequence (GS) have been introduced during generation of the recombinant protein (tag residues). The last five residues (KKASS) are flexible.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prss12, Bssp3 / Plasmid: pCIOX / Details (production host): Addgene #51300 / Production host: Escherichia coli (E. coli) / Strain (production host): Shuffle T7
References: UniProt: O08762, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 3.24 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 16% PEG 3350, 0.1 M Tri-soidium citrate / Temp details: cold room

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.983 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.983 Å / Relative weight: 1
ReflectionResolution: 1.7→42.6 Å / Num. obs: 34576 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Net I/σ(I): 15.5
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 6.9 % / Rmerge(I) obs: 2.84 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 1785 / CC1/2: 0.434 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BY2

1by2


Resolution: 1.7→42.58 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / SU B: 4.836 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21306 1725 5 %RANDOM
Rwork0.18992 ---
obs0.19122 32795 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.813 Å2
Baniso -1Baniso -2Baniso -3
1-2.91 Å20 Å20 Å2
2---0.4 Å20 Å2
3----2.5 Å2
Refinement stepCycle: 1 / Resolution: 1.7→42.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1654 0 0 85 1739
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0141701
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171479
X-RAY DIFFRACTIONr_angle_refined_deg1.6991.6552291
X-RAY DIFFRACTIONr_angle_other_deg1.041.6583478
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.235214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.10322100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48915291
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3991514
X-RAY DIFFRACTIONr_chiral_restr0.0830.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021972
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02316
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.664.163859
X-RAY DIFFRACTIONr_mcbond_other3.664.156858
X-RAY DIFFRACTIONr_mcangle_it5.546.2011072
X-RAY DIFFRACTIONr_mcangle_other5.5386.211073
X-RAY DIFFRACTIONr_scbond_it4.0414.631842
X-RAY DIFFRACTIONr_scbond_other4.0094.61840
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1466.7381219
X-RAY DIFFRACTIONr_long_range_B_refined8.74747.2821830
X-RAY DIFFRACTIONr_long_range_B_other8.76147.2261822
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3063 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.412 112 -
Rwork0.363 2397 -
obs--99.92 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.9291.9781-4.31293.6931-4.786910.03210.13050.14110.31540.04870.0848-0.0034-0.0706-0.0078-0.21530.015-0.00740.00590.02670.00670.036530.475436.349312.6859
212.2691-9.7771-7.291111.03671.231510.9105-0.1726-0.1129-0.22610.42510.53930.6264-0.2586-0.6336-0.36670.03960.01040.07260.1314-0.01180.190424.33531.275323.6738
32.6888-1.07121.57142.8754-1.93074.4992-0.16480.07540.36490.0551-0.0496-0.222-0.34660.21680.21440.0477-0.03950.0030.0399-0.02110.083534.98636.24717.5111
44.1175-2.26420.41277.1761-1.48592.967-0.130.0404-0.02250.0410.02950.00670.07860.04740.10050.0143-0.00650.00980.0474-0.02680.022436.680827.43924.3596
53.24110.79612.81756.3041-4.669.45480.13740.62650.0001-0.4843-0.0657-0.04150.38440.4268-0.07170.11280.04380.07020.1854-0.01670.075737.189327.2869.6713
63.7672-0.4884-1.10229.8748.53028.04970.18240.43710.2241-0.27120.14-0.8166-0.44440.2562-0.32240.091-0.0805-0.08290.17910.1410.411146.233140.161117.372
75.45151.3065-1.71533.20711.089312.3755-0.69640.59451.09540.1314-0.0039-0.005-0.41950.21470.70030.2551-0.1616-0.21080.10970.16480.393637.972745.962917.2572
81.492-0.54732.15887.05290.39013.3345-0.09660.40410.144-0.30430.0263-0.8241-0.16170.63270.07040.11740.01750.04850.1969-0.01390.137141.835131.821316.8137
93.3533-0.38630.28166.5115-1.43870.4946-0.05490.1095-0.0578-0.2223-0.0263-0.13790.1230.13950.08130.10430.02450.0320.2075-0.01340.094443.349322.11127.4675
104.06512.16070.84854.11340.47741.27120.1035-0.2619-0.52210.4411-0.0829-0.31070.40310.1993-0.02060.19070.08610.00220.17220.01110.113244.079116.188233.8923
114.51030.77750.94513.6791-0.04034.13560.0219-0.2267-0.16080.4502-0.0008-0.21560.27680.2979-0.02110.07930.0366-0.02620.142-0.02090.02444.967921.558534.9922
125.6995-1.68232.708813.18261.79511.83430.2816-0.5289-0.90310.81120.1201-0.10340.3088-0.253-0.40170.33190.1619-0.10040.3320.10010.560350.75128.47135.3155
132.9451-0.67380.53414.14161.13244.63490.1616-0.6567-0.81940.9222-0.2724-0.19090.75970.31290.11080.38120.0106-0.12880.42940.17010.3844.609215.016139.1863
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 7
2X-RAY DIFFRACTION2A8 - 13
3X-RAY DIFFRACTION3A14 - 51
4X-RAY DIFFRACTION4A52 - 59
5X-RAY DIFFRACTION5A60 - 69
6X-RAY DIFFRACTION6A70 - 74
7X-RAY DIFFRACTION7A75 - 82
8X-RAY DIFFRACTION8A83 - 106
9X-RAY DIFFRACTION9B1 - 13
10X-RAY DIFFRACTION10B14 - 44
11X-RAY DIFFRACTION11B45 - 68
12X-RAY DIFFRACTION12B69 - 79
13X-RAY DIFFRACTION13B80 - 106

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