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- PDB-1m9u: Crystal Structure of Earthworm Fibrinolytic Enzyme Component A fr... -

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Basic information

Entry
Database: PDB / ID: 1m9u
TitleCrystal Structure of Earthworm Fibrinolytic Enzyme Component A from Eisenia fetida
ComponentsEarthworm Fibrinolytic Enzyme
KeywordsHYDROLASE / SERINE PROTEASE (ELASTASE-LIKE) / FIBRINOLYTIC ENZYME
Function / homology
Function and homology information


kinase activity / serine-type endopeptidase activity / proteolysis
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Fibrinolytic enzyme component A
Similarity search - Component
Biological speciesEisenia fetida (common brandling worm)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.3 Å
AuthorsChang, W. / Liang, D. / Tang, Y.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Crystal structure of earthworm fibrinolytic enzyme component a: revealing the structural determinants of its dual fibrinolytic activity.
Authors: Tang, Y. / Liang, D. / Jiang, T. / Zhang, J. / Gui, L. / Chang, W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and Preliminary X-ray Analysis of Earthworm Fibrinolytic Enzyme Component A from Eisenia fetida
Authors: Tang, Y. / Zhang, J. / Gui, L. / Wu, C. / Fan, R. / Chang, W. / Liang, D.
#2: Journal: ENZYMES 3RD ED. / Year: 1971
Title: Pancreatic Elastase
Authors: Hartley, B.S. / Shotton, D.M.
History
DepositionJul 29, 2002Deposition site: RCSB / Processing site: PDBJ
SupersessionAug 14, 2002ID: 1IJ7
Revision 1.0Aug 14, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Earthworm Fibrinolytic Enzyme
B: Earthworm Fibrinolytic Enzyme
C: Earthworm Fibrinolytic Enzyme


Theoretical massNumber of molelcules
Total (without water)73,9863
Polymers73,9863
Non-polymers00
Water5,008278
1
A: Earthworm Fibrinolytic Enzyme


Theoretical massNumber of molelcules
Total (without water)24,6621
Polymers24,6621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Earthworm Fibrinolytic Enzyme


Theoretical massNumber of molelcules
Total (without water)24,6621
Polymers24,6621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Earthworm Fibrinolytic Enzyme


Theoretical massNumber of molelcules
Total (without water)24,6621
Polymers24,6621
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.600, 126.100, 129.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Earthworm Fibrinolytic Enzyme


Mass: 24661.951 Da / Num. of mol.: 3 / Fragment: component A / Source method: isolated from a natural source / Source: (natural) Eisenia fetida (common brandling worm)
References: UniProt: Q8MX72, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: Ammonium Sulfate, PEG400, MOPS, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Details: Otwinowski, Z., (1997) Methods Enzymol., 276, 307.

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SEALED TUBE / Type: CONVENTIONAL Cu / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 15, 2000 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→9 Å / Num. all: 29792 / Num. obs: 29703 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 16 % / Biso Wilson estimate: 32.99 Å2 / Rmerge(I) obs: 0.156 / Net I/σ(I): 16.2
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 2.4 / % possible all: 98.9
Reflection
*PLUS
Rmerge(I) obs: 0.162
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 98.9 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MIR / Resolution: 2.3→9 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: NCS RESTRAINED
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2381 8 %RANDOM
Rwork0.191 ---
all-29792 --
obs-29703 99.7 %-
Displacement parametersBiso mean: 19.2 Å2
Refinement stepCycle: LAST / Resolution: 2.3→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5187 0 0 278 5465
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_angle_deg1.633
LS refinement shellResolution: 2.3→2.4 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3802 249 -
Rwork0.3055 3343 -
obs-3592 97.8 %
Refinement
*PLUS
Highest resolution: 2.3 Å / % reflection Rfree: 8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.63
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.14
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.87

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