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- PDB-3fgq: Crystal structure of native human neuroserpin -

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Basic information

Entry
Database: PDB / ID: 3fgq
TitleCrystal structure of native human neuroserpin
ComponentsNeuroserpin
KeywordsHYDROLASE INHIBITOR / serpin / polymerization / dementia / tPA / inhibitor / 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: 2.09 Å
AuthorsTakehara, S. / Yang, X. / Mikami, B. / Onda, M.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: The 2.1-A crystal structure of native neuroserpin reveals unique structural elements that contribute to conformational instability
Authors: Takehara, S. / Onda, M. / Zhang, J. / Nishiyama, M. / Yang, X. / Mikami, B. / Lomas, D.A.
History
DepositionDec 8, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Neuroserpin
B: Neuroserpin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,3904
Polymers90,2062
Non-polymers1842
Water5,332296
1
A: Neuroserpin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1952
Polymers45,1031
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Neuroserpin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1952
Polymers45,1031
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.017, 51.953, 80.316
Angle α, β, γ (deg.)90.09, 90.05, 97.12
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 22:353 or resseq 359:400 )
21chain B and (resseq 22:353 or resseq 359:400 )

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROALAALAAA22 - 35319 - 350
12ALAALAMETMETAA359 - 400356 - 397
21PROPROALAALABB22 - 35319 - 350
22ALAALAMETMETBB359 - 400356 - 397

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Components

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


Mass: 45103.039 Da / Num. of mol.: 2 / Fragment: UNP residues 17-400
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pQE81L / Production host: Escherichia coli (E. coli) / References: UniProt: Q99574
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% PEG 4000, 20% iso-propanol, 0.1M sodium citrate buffer , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 9, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. obs: 41751 / % possible obs: 96.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 24
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 1.9 / Num. unique all: 11147 / % possible all: 91.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B3K

1b3k


Resolution: 2.09→45.662 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.31 / SU R Cruickshank DPI: 10.04 / Phase error: 23.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2258 2084 4.99 %RANDOM
Rwork0.1733 ---
obs0.176 41751 95.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.662 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 136.74 Å2 / Biso mean: 39.013 Å2
Baniso -1Baniso -2Baniso -3
1--1.265 Å2-1.133 Å2-0.01 Å2
2--1.915 Å2-0.556 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 2.09→45.662 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5995 0 12 296 6303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016171
X-RAY DIFFRACTIONf_angle_d1.3078331
X-RAY DIFFRACTIONf_chiral_restr0.081908
X-RAY DIFFRACTIONf_plane_restr0.0051088
X-RAY DIFFRACTIONf_dihedral_angle_d19.4752273
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3028X-RAY DIFFRACTIONPOSITIONAL
12B3028X-RAY DIFFRACTIONPOSITIONAL0.056
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0896-2.13820.28931120.21842150X-RAY DIFFRACTION79
2.1382-2.19160.28171320.21162609X-RAY DIFFRACTION93
2.1916-2.25090.28881260.20032628X-RAY DIFFRACTION94
2.2509-2.31710.24051560.18282623X-RAY DIFFRACTION95
2.3171-2.39190.24771350.1792604X-RAY DIFFRACTION95
2.3919-2.47740.26761500.18132632X-RAY DIFFRACTION95
2.4774-2.57660.28191270.18612700X-RAY DIFFRACTION96
2.5766-2.69380.26211250.18372658X-RAY DIFFRACTION97
2.6938-2.83580.2681410.1962698X-RAY DIFFRACTION97
2.8358-3.01350.26831310.19652692X-RAY DIFFRACTION98
3.0135-3.24610.2341460.18472746X-RAY DIFFRACTION98
3.2461-3.57260.21451430.1622738X-RAY DIFFRACTION99
3.5726-4.08930.20341410.14272718X-RAY DIFFRACTION99
4.0893-5.1510.16421720.12882729X-RAY DIFFRACTION99
5.151-45.67330.17971470.15712742X-RAY DIFFRACTION99

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