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- PDB-3f5n: Structure of native human neuroserpin -

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Basic information

Entry
Database: PDB / ID: 3f5n
TitleStructure of native human neuroserpin
ComponentsNeuroserpin
KeywordsHYDROLASE INHIBITOR / neuroserpin / serpin / cleaved form / fenib / human / tissue plasminogen activator
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: 3.15 Å
AuthorsRicagno, S. / Caccia, S. / Sorrentino, G. / 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
DepositionNov 4, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 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
B: Neuroserpin
C: Neuroserpin
D: Neuroserpin
E: Neuroserpin


Theoretical massNumber of molelcules
Total (without water)231,6015
Polymers231,6015
Non-polymers00
Water0
1
A: Neuroserpin


Theoretical massNumber of molelcules
Total (without water)46,3201
Polymers46,3201
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neuroserpin


Theoretical massNumber of molelcules
Total (without water)46,3201
Polymers46,3201
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Neuroserpin


Theoretical massNumber of molelcules
Total (without water)46,3201
Polymers46,3201
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Neuroserpin


Theoretical massNumber of molelcules
Total (without water)46,3201
Polymers46,3201
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Neuroserpin


Theoretical massNumber of molelcules
Total (without water)46,3201
Polymers46,3201
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)171.796, 179.176, 248.263
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A26 - 103
2115B26 - 103
1214A109 - 233
2214B109 - 233
1314A242 - 262
2314B242 - 262
1414A266 - 353
2414B266 - 353
1514A373 - 383
2514B373 - 383
1614A389 - 402
2614B389 - 402
1124A26 - 85
2124C26 - 85
1224A94 - 102
2224C94 - 102
1324A108 - 228
2324C108 - 228
1424A248 - 259
2424C248 - 259
1524A291 - 351
2524C291 - 351
1624A372 - 402
2624C372 - 402
1134A26 - 103
2134D26 - 103
1234A109 - 233
2234D109 - 233
1334A243 - 353
2334D243 - 353
1434A368 - 400
2434D368 - 400
1144A26 - 231
2144E26 - 231
1244A235 - 353
2244E235 - 353
1344A368 - 400
2344E368 - 400

NCS ensembles :
ID
1
2
3
4

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Components

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


Mass: 46320.273 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SERPINI1, PI12 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLys / References: UniProt: Q99574

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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: 4.12 Å3/Da / Density % sol: 70.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: Ammonium sulphate, Na cacodylate, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 9, 2007 / Details: Toroidal Zerodur mirror
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: 3.15→20 Å / Num. obs: 66051 / % possible obs: 99.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 89.5 Å2 / Rmerge(I) obs: 0.129 / Rsym value: 0.129 / Net I/σ(I): 10.3
Reflection shellResolution: 3.15→3.32 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.834 / Mean I/σ(I) obs: 1.9 / Num. unique all: 9605 / Rsym value: 0.834 / % possible all: 100

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Processing

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

1jjo


Resolution: 3.15→19.98 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.871 / SU B: 51.266 / SU ML: 0.39 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.329 / ESU R Free: 0.437 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28315 3356 5.1 %RANDOM
Rwork0.23415 ---
obs0.23655 62671 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 86.665 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2---0.08 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 3.15→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14513 0 0 0 14513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02214796
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.9519960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.50551778
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26925.121746
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.766152644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4081565
X-RAY DIFFRACTIONr_chiral_restr0.1020.22202
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111164
X-RAY DIFFRACTIONr_mcbond_it0.391.58960
X-RAY DIFFRACTIONr_mcangle_it0.731214467
X-RAY DIFFRACTIONr_scbond_it0.74835836
X-RAY DIFFRACTIONr_scangle_it1.3274.55493
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2354medium positional0.420.5
21A2243medium positional0.420.5
31A2704medium positional0.390.5
41A2682medium positional0.430.5
12B255loose positional0.545
11A2354medium thermal0.462
22C2243medium thermal0.492
32D2704medium thermal0.352
42E2682medium thermal0.342
12B255loose thermal0.3910
LS refinement shellResolution: 3.15→3.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 253 -
Rwork0.334 4468 -
obs--99.68 %
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)
10.8984-1.76760.64737.9034-0.70971.77020.0893-0.0247-0.02450.39430.01321.26390.0263-0.3316-0.1025-0.7319-0.06150.0462-0.1619-0.04320.0969-58.425380.4616-54.4106
27.66284.0341.24722.69650.2781.28870.3249-0.3027-0.64010.0178-0.2365-0.5543-0.1268-0.0774-0.0884-0.2906-0.0318-0.0032-0.14180.0424-0.0175-6.751470.5381-43.1732
30.68210.8809-0.23097.8335-0.99571.3240.1027-0.06140.02590.5486-0.0950.6185-0.44730.1113-0.0076-0.4333-0.0019-0.0119-0.2121-0.0531-0.2052-48.440824.5393-61.361
41.1417-0.36761.32081.3824-1.50258.29010.09630.0620.0537-0.1593-0.1765-0.13690.90310.85040.08010.1915-0.01430.0277-0.1381-0.032-0.2607-36.374437.2915-14.8077
50.77080.3633-1.18031.2208-0.80367.5192-0.0182-0.03620.06380.1608-0.0624-0.2627-1.31591.23730.08060.4887-0.525-0.06320.1055-0.0035-0.2166-26.95160.8532-106.7744
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 400
2X-RAY DIFFRACTION2B26 - 407
3X-RAY DIFFRACTION3C26 - 399
4X-RAY DIFFRACTION4D26 - 399
5X-RAY DIFFRACTION5E26 - 399

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