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- PDB-3f02: Cleaved human neuroserpin -

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Basic information

Entry
Database: PDB / ID: 3f02
TitleCleaved human neuroserpin
Components(Neuroserpin) x 2
KeywordsHYDROLASE INHIBITOR / neuroserpin / serpin / cleaved form / fenib / human / Disease mutation / Glycoprotein / Protease inhibitor / Secreted / Serine protease inhibitor
Function / homology
Function and homology information


cytoplasmic vesicle lumen / peripheral nervous system development / central nervous system development / serine-type endopeptidase inhibitor activity / positive regulation of neuron projection development / perikaryon / secretory granule lumen / neuronal cell body / extracellular space / extracellular exosome
Similarity search - Function
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 ...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 / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRicagno, S. / Sorrentino, G. / Caccia, S. / Bolognesi, M.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Human neuroserpin: structure and time-dependent inhibition
Authors: Ricagno, S. / Caccia, S. / Sorrentino, G. / Antonini, G. / Bolognesi, M.
History
DepositionOct 24, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Apr 16, 2014Group: Refinement description
Revision 1.3Nov 1, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuroserpin
C: Neuroserpin
B: Neuroserpin
D: Neuroserpin


Theoretical massNumber of molelcules
Total (without water)92,6774
Polymers92,6774
Non-polymers00
Water9,926551
1
A: Neuroserpin
C: Neuroserpin


Theoretical massNumber of molelcules
Total (without water)46,3382
Polymers46,3382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-33 kcal/mol
Surface area15640 Å2
MethodPISA
2
B: Neuroserpin
D: Neuroserpin


Theoretical massNumber of molelcules
Total (without water)46,3382
Polymers46,3382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-31 kcal/mol
Surface area16060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.928, 100.066, 115.825
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsIN THIS ENTRY, NEUROSERPIN WAS CLEAVED BY TRYPSIN AND SPLIT TO TWO PARTS. ENTIRE NEUROSERPIN SHOULD FORM MONOMER.

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Components

#1: Protein Neuroserpin / Serpin I1 / Protease inhibitor 12


Mass: 40665.719 Da / Num. of mol.: 2 / Fragment: residues 17-362
Source method: isolated from a genetically manipulated source
Details: Cleaved neurserpin by trypsin / Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINI1, PI12 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLys / References: UniProt: Q99574
#2: Protein/peptide Neuroserpin / Serpin I1 / Protease inhibitor 12


Mass: 5672.606 Da / Num. of mol.: 2 / Fragment: residues 363-410
Source method: isolated from a genetically manipulated source
Details: Cleaved neurserpin by trypsin / Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINI1, PI12 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLys / References: UniProt: Q99574
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 551 / 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: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Ammonium sulphate, Na acetate, PEG MME 2000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 5, 2008
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→40 Å / Num. obs: 78887 / % possible obs: 99.6 % / Redundancy: 7 % / Biso Wilson estimate: 20.34 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 13
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2 / % possible all: 97.3

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASESphasing
REFMAC5.4.0069refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JJO

1jjo


Resolution: 1.8→19.72 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.071 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23511 3961 5 %RANDOM
Rwork0.19101 ---
obs0.19322 74815 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.111 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5788 0 0 551 6339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226056
X-RAY DIFFRACTIONr_bond_other_d0.0010.024091
X-RAY DIFFRACTIONr_angle_refined_deg1.4741.9548202
X-RAY DIFFRACTIONr_angle_other_deg1.378310017
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5295756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86125.098306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.555151099
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9761527
X-RAY DIFFRACTIONr_chiral_restr0.0780.2903
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026751
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021234
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_it0.7631.53654
X-RAY DIFFRACTIONr_mcbond_other0.1941.51478
X-RAY DIFFRACTIONr_mcangle_it1.38825920
X-RAY DIFFRACTIONr_scbond_it2.24832402
X-RAY DIFFRACTIONr_scangle_it3.6074.52260
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 284 -
Rwork0.268 5217 -
obs--95.62 %
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)
11.28420.0285-0.40041.0769-1.56853.90960.1326-0.12250.22190.5264-0.0945-0.1057-0.53150.1428-0.03810.1326-0.0695-0.0252-0.0771-0.0128-0.015923.410413.373968.6582
20.2144-0.02680.00341.4423-1.11861.16790.0279-0.0351-0.060.28610.1460.2388-0.1663-0.1196-0.1740.03230.0370.0499-0.05240.0098-0.0349.38032.862566.7329
30.6157-0.10590.29842.1041-0.39121.0495-0.0104-0.00160.06080.0239-0.0286-0.1221-0.07460.0970.039-0.0433-0.00950.0081-0.04690.0009-0.057119.882320.010844.1372
40.24820.02030.11851.4184-1.16092.15860.0159-0.0541-0.02090.2781-0.0442-0.0256-0.16070.08440.02830.0185-0.0036-0.0015-0.05120.0031-0.063920.38228.810260.8881
51.0467-0.1899-0.18421.2294-0.82681.99060.08280.1434-0.0441-0.2829-0.0957-0.0650.36770.02880.0129-0.01860.04620.02570.00630.02690.003922.682121.1651104.8699
60.1255-0.0557-0.04490.9895-0.71161.03540.02190.01280.0389-0.11450.05560.13340.0468-0.0812-0.0776-0.0694-0.019-0.0212-0.00920.01780.00198.961131.8077107.5343
70.75410.0632-0.29621.1974-0.28850.9442-0.00640.0152-0.00780.0641-0.0103-0.08710.10420.07850.0167-0.06790.01-0.0054-0.02010-0.030619.96114.8081129.3141
80.0848-0.18090.12950.9409-0.88562.08250.04070.07010.0584-0.088-0.0659-0.03690.09010.14520.0251-0.09150.00760.00530.00340.0194-0.019420.02125.9403112.9984
90.01090.0037-0.02140.0380.0780.23950.0034-0.00270.0069-0.0177-0.0039-0.01020.03250.02120.00050.00310.0082-0.00510.02630.00920.049616.468518.093887.1903
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 93
2X-RAY DIFFRACTION2A104 - 200
3X-RAY DIFFRACTION3A201 - 300
4X-RAY DIFFRACTION4A302 - 362
5X-RAY DIFFRACTION4C365 - 399
6X-RAY DIFFRACTION5B24 - 94
7X-RAY DIFFRACTION6B102 - 200
8X-RAY DIFFRACTION7B201 - 301
9X-RAY DIFFRACTION8B302 - 362
10X-RAY DIFFRACTION8D364 - 400
11X-RAY DIFFRACTION9A363 - 705
12X-RAY DIFFRACTION9B1 - 3
13X-RAY DIFFRACTION9B363 - 707
14X-RAY DIFFRACTION9C17
15X-RAY DIFFRACTION9C418 - 536
16X-RAY DIFFRACTION9D5 - 13
17X-RAY DIFFRACTION9D426 - 667

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