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- PDB-8zvx: Crystal structure of snFPITE-n2 -

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Basic information

Entry
Database: PDB / ID: 8zvx
TitleCrystal structure of snFPITE-n2
Components
  • snFPITE-n2 A chain
  • snFPITE-n2 B chain
KeywordsBLOOD CLOTTING / fibrin lysis / fibrinogen lysis / plasminogen activation / proteinase
Function / homologyphenylmethanesulfonic acid
Function and homology information
Biological speciesSipunculus nudus (marine worm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsChen, X. / Yang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21807088 China
CitationJournal: Nat Commun / Year: 2025
Title: A facultative plasminogen-independent thrombolytic enzyme from Sipunculus nudus.
Authors: Tang, M. / Ma, G. / Xu, C. / Yang, H. / Lin, H. / Bian, C. / Hu, C. / Lu, M. / Chen, L. / Jie, W. / Yue, Z. / Jian, J. / Sun, Y. / Yan, H. / Zhou, J. / Zhang, X. / Liao, S. / Li, Z. / Cai, S. ...Authors: Tang, M. / Ma, G. / Xu, C. / Yang, H. / Lin, H. / Bian, C. / Hu, C. / Lu, M. / Chen, L. / Jie, W. / Yue, Z. / Jian, J. / Sun, Y. / Yan, H. / Zhou, J. / Zhang, X. / Liao, S. / Li, Z. / Cai, S. / Wu, Y. / Yang, K. / Xiong, Y. / Zhao, Y. / Lv, Z. / Xu, X. / Liu, C. / Xin, P. / Ye, L. / Cui, X. / Shi, Q. / Chen, X. / Xu, R.
History
DepositionJun 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: snFPITE-n2 A chain
B: snFPITE-n2 B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,37513
Polymers50,0392
Non-polymers1,33511
Water8,017445
1
A: snFPITE-n2 A chain
hetero molecules

B: snFPITE-n2 B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,37513
Polymers50,0392
Non-polymers1,33511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area4430 Å2
ΔGint-54 kcal/mol
Surface area17630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.262, 59.738, 193.702
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein snFPITE-n2 A chain


Mass: 25085.912 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sipunculus nudus (marine worm) / Production host: Sipunculus nudus (marine worm)
#2: Protein snFPITE-n2 B chain


Mass: 24953.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sipunculus nudus (marine worm) / Production host: Sipunculus nudus (marine worm)

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Non-polymers , 5 types, 456 molecules

#3: Chemical ChemComp-PMS / phenylmethanesulfonic acid


Mass: 172.202 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8O3S
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 445 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.93 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion
Details: 2 M Lithium sulfate, 100 mM Tris, pH 8.5, 2% v/v Polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.5→96.851 Å / Num. obs: 71302 / % possible obs: 96 % / Redundancy: 5.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.035 / Rrim(I) all: 0.085 / Net I/σ(I): 12.6
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.686 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 3616 / CC1/2: 0.821 / Rpim(I) all: 0.313 / Rrim(I) all: 0.756 / Χ2: 1.05 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→96.851 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.186 3435 4.82 %
Rwork0.1628 --
obs0.164 71196 95.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→96.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3500 0 88 445 4033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123673
X-RAY DIFFRACTIONf_angle_d1.1624997
X-RAY DIFFRACTIONf_dihedral_angle_d18.6141271
X-RAY DIFFRACTIONf_chiral_restr0.096543
X-RAY DIFFRACTIONf_plane_restr0.008660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.52050.25481340.21822803X-RAY DIFFRACTION100
1.5205-1.54230.29891210.21922756X-RAY DIFFRACTION100
1.5423-1.56530.21191390.20432791X-RAY DIFFRACTION100
1.5653-1.58980.22621580.2032766X-RAY DIFFRACTION100
1.5898-1.61580.22061260.19032804X-RAY DIFFRACTION100
1.6158-1.64370.21621670.17772759X-RAY DIFFRACTION100
1.6437-1.67360.19131300.18052772X-RAY DIFFRACTION100
1.6736-1.70580.20741380.18852486X-RAY DIFFRACTION99
1.7058-1.74060.0987180.2027375X-RAY DIFFRACTION89
1.7406-1.77840.21821390.1722823X-RAY DIFFRACTION100
1.7784-1.81980.19881490.17342772X-RAY DIFFRACTION100
1.8198-1.86530.19181530.17082816X-RAY DIFFRACTION100
1.8653-1.91580.21251440.16262743X-RAY DIFFRACTION100
1.9158-1.97210.19361310.1612862X-RAY DIFFRACTION100
1.9721-2.03580.17111340.15472789X-RAY DIFFRACTION100
2.0358-2.10860.19821290.15452824X-RAY DIFFRACTION100
2.1086-2.1930.18261350.15322827X-RAY DIFFRACTION100
2.193-2.29280.17711320.15992842X-RAY DIFFRACTION100
2.2928-2.41370.18591500.16192793X-RAY DIFFRACTION100
2.4137-2.5650.22141470.16662834X-RAY DIFFRACTION100
2.565-2.7630.18991400.16692850X-RAY DIFFRACTION100
2.763-3.04110.18121420.16652873X-RAY DIFFRACTION100
3.0411-3.48110.17241530.15452854X-RAY DIFFRACTION99
3.4811-4.38590.16541630.13972912X-RAY DIFFRACTION100
4.3859-96.8510.16271630.15963035X-RAY DIFFRACTION99

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