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- PDB-8zvs: Crystal structure of snFPITE-n1 -

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Basic information

Entry
Database: PDB / ID: 8zvs
TitleCrystal structure of snFPITE-n1
ComponentssnFPITE-n1
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: 1.987 Å
AuthorsChen, X. / Yang, H. / Hu, Y.L.
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

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Assembly

Deposited unit
A: snFPITE-n1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2223
Polymers24,9541
Non-polymers2682
Water4,288238
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-9 kcal/mol
Surface area9510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.315, 43.730, 121.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-410-

HOH

21A-601-

HOH

31A-604-

HOH

41A-630-

HOH

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Components

#1: Protein snFPITE-n1


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)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PMS / phenylmethanesulfonic acid


Mass: 172.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
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: 2.15 Å3/Da / Density % sol: 42.73 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / Details: 0.1 M Tris, pH 9.0, 2 M (NH4)2SO4, 0.2 M NaSCN

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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: Nov 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.987→43.73 Å / Num. obs: 15359 / % possible obs: 99.2 % / Redundancy: 3.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.021 / Rpim(I) all: 0.014 / Rrim(I) all: 0.025 / Net I/σ(I): 24.6
Reflection shellResolution: 1.99→2.04 Å / Rmerge(I) obs: 0.034 / Mean I/σ(I) obs: 14.9 / Num. unique obs: 1008 / CC1/2: 0.997 / Rpim(I) all: 0.026 / Rrim(I) all: 0.043 / % possible all: 95.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.987→38.266 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 18.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2047 727 4.75 %
Rwork0.1563 --
obs0.1586 15312 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.987→38.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1749 0 15 238 2002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021804
X-RAY DIFFRACTIONf_angle_d0.4882461
X-RAY DIFFRACTIONf_dihedral_angle_d2.8451033
X-RAY DIFFRACTIONf_chiral_restr0.043267
X-RAY DIFFRACTIONf_plane_restr0.004331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9871-2.14050.20041340.14662830X-RAY DIFFRACTION98
2.1405-2.35590.22271200.162845X-RAY DIFFRACTION98
2.3559-2.69680.2381400.17982923X-RAY DIFFRACTION100
2.6968-3.39730.21321670.17412922X-RAY DIFFRACTION100
3.3973-38.2660.18271660.1383065X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 10.2516 Å / Origin y: 1.1052 Å / Origin z: 14.8202 Å
111213212223313233
T0.1593 Å20.0038 Å20.0003 Å2-0.1604 Å20.0009 Å2--0.1583 Å2
L0.428 °2-0.0992 °2-0.0187 °2-0.2654 °2-0.0548 °2--0.271 °2
S0.0028 Å °0.008 Å °-0.011 Å °0.0067 Å °0.0004 Å °-0.0205 Å °-0.0088 Å °-0.0157 Å °-0 Å °
Refinement TLS groupSelection details: all

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