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- PDB-3uir: Crystal structure of the plasmin-textilinin-1 complex -

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Basic information

Entry
Database: PDB / ID: 3uir
TitleCrystal structure of the plasmin-textilinin-1 complex
Components
  • Plasmin light chain B
  • Textilinin-1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / serine protease / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


suppression of blood coagulation in another organism / plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / mononuclear cell migration / Signaling by PDGF / negative regulation of cell-cell adhesion mediated by cadherin ...suppression of blood coagulation in another organism / plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / trophoblast giant cell differentiation / tissue remodeling / protein antigen binding / tissue regeneration / mononuclear cell migration / Signaling by PDGF / negative regulation of cell-cell adhesion mediated by cadherin / positive regulation of fibrinolysis / Dissolution of Fibrin Clot / negative regulation of cell-substrate adhesion / myoblast differentiation / biological process involved in interaction with symbiont / labyrinthine layer blood vessel development / muscle cell cellular homeostasis / Activation of Matrix Metalloproteinases / apolipoprotein binding / extracellular matrix disassembly / positive regulation of blood vessel endothelial cell migration / negative regulation of fibrinolysis / fibrinolysis / Degradation of the extracellular matrix / serine-type peptidase activity / platelet alpha granule lumen / serine-type endopeptidase inhibitor activity / Schaffer collateral - CA1 synapse / kinase binding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / Platelet degranulation / protein-folding chaperone binding / toxin activity / protease binding / collagen-containing extracellular matrix / endopeptidase activity / blood microparticle / protein domain specific binding / negative regulation of cell population proliferation / external side of plasma membrane / serine-type endopeptidase activity / signaling receptor binding / glutamatergic synapse / enzyme binding / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Peptidase S1A, plasmin / divergent subfamily of APPLE domains / : / : / Pancreatic trypsin inhibitor Kunitz domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site ...Peptidase S1A, plasmin / divergent subfamily of APPLE domains / : / : / Pancreatic trypsin inhibitor Kunitz domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / Few Secondary Structures / Irregular / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / 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
Plasminogen / Kunitz-type serine protease inhibitor textilinin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Pseudonaja textilis textilis (cobra)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.777 Å
AuthorsGuddat, L.W. / Millers, E.K. / de jersey, J. / Lavin, M.F. / Masci, P.M.
CitationJournal: Plos One / Year: 2013
Title: The structure of human microplasmin in complex with textilinin-1, an aprotinin-like inhibitor from the Australian brown snake.
Authors: Millers, E.K. / Johnson, L.A. / Birrell, G.W. / Masci, P.P. / Lavin, M.F. / de Jersey, J. / Guddat, L.W.
History
DepositionNov 5, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Plasmin light chain B
B: Plasmin light chain B
C: Textilinin-1
D: Textilinin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7816
Polymers67,5894
Non-polymers1922
Water1,874104
1
A: Plasmin light chain B
C: Textilinin-1


Theoretical massNumber of molelcules
Total (without water)33,7952
Polymers33,7952
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-6 kcal/mol
Surface area12240 Å2
MethodPISA
2
B: Plasmin light chain B
D: Textilinin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9874
Polymers33,7952
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-26 kcal/mol
Surface area12890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.901, 48.019, 82.627
Angle α, β, γ (deg.)90.00, 102.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Plasmin light chain B / microplasmin


Mass: 27096.135 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P00747, plasmin
#2: Protein Textilinin-1 / Txln-1


Mass: 6698.442 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudonaja textilis textilis (cobra) / Production host: Escherichia coli (E. coli) / References: UniProt: Q90WA1
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.35 Å3/Da / Density % sol: 47.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.17M ammonium sulfate, 25.5% PEG 4000, 15% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 5, 2007
RadiationMonochromator: yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.777→41.6 Å / Num. obs: 15858 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 7.9
Reflection shellResolution: 2.78→2.89 Å / Rmerge(I) obs: 0.284 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.284 / % possible all: 99.3

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Processing

Software
NameVersionClassification
CrystalCleardata collection
EPMRphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.777→39.55 Å / SU ML: 0.31 / σ(F): 1.37 / Phase error: 22.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.258 800 5.05 %
Rwork0.2087 --
obs0.2111 15849 97.74 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.1969 Å20 Å2-0.06 Å2
2---0.9284 Å2-0 Å2
3---0.7315 Å2
Refinement stepCycle: LAST / Resolution: 2.777→39.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4558 0 10 104 4672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044703
X-RAY DIFFRACTIONf_angle_d0.9056385
X-RAY DIFFRACTIONf_dihedral_angle_d14.1221681
X-RAY DIFFRACTIONf_chiral_restr0.057697
X-RAY DIFFRACTIONf_plane_restr0.004834
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7773-2.95130.31091430.2551219587
2.9513-3.17910.30251190.24752561100
3.1791-3.49880.26231330.21332515100
3.4988-4.00470.27231370.19212561100
4.0047-5.04380.21851190.17162584100
5.0438-39.55440.23411490.22312633100
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)
10.40850.1493-0.03840.0894-0.00910.21060.2172-0.0966-0.1578-0.77050.0869-0.18080.1973-0.12490.17230.28610.09120.26120.142-0.03260.168560.184844.946738.6916
20.051-0.02450.04260.1293-0.07390.1163-0.2649-0.0622-0.189-0.4998-0.304-0.08630.48420.0589-0.03350.26220.01070.03610.1730.03040.201459.774549.781837.6348
30.08030.06390.00280.04090.00650.0276-0.0574-0.0029-0.31750.01550.17660.08670.2782-0.14730.0886-0.3868-0.0723-0.20130.24130.06660.504530.712634.348652.1926
40.37390.10850.05990.8137-0.12390.1695-0.1058-0.01280.1648-0.4346-0.03810.33120.0171-0.19130.0210.20510.0324-0.10610.21990.02130.330835.782346.310150.2827
50.5515-0.0385-0.14940.4760.34930.3144-0.02420.14420.2875-0.2246-0.0634-0.1524-0.1782-0.0617-0.02620.21340.024-0.00730.1696-0.01370.245439.86253.238253.598
60.4719-0.2079-0.2320.39980.56680.9145-0.1981-0.3885-0.36520.56180.10780.89930.4634-0.1428-0.1370.1068-0.1411-0.09490.22910.07650.335935.797237.379961.4308
70.48880.1346-0.03190.4431-0.20180.15930.0717-0.0291-0.0268-0.0210.0118-0.0279-0.07670.0111-0.00010.13890.0097-0.00490.15910.00160.139345.60436.030857.1127
80.05750.0566-0.05020.13680.04190.1812-0.0444-0.15410.04290.02510.0718-0.1420.01020.12540.05630.36520.0362-0.16320.2489-0.05160.327193.088640.013137.7348
90.1182-0.0839-0.07870.01250.08180.0899-0.0434-0.0492-0.0029-0.03240.00430.09040.0939-0.1149-0.06580.232-0.0103-0.05430.1606-0.01650.192381.30637.626127.6587
100.1251-0.0281-0.04920.01490.00890.0147-0.1285-0.16080.07990.0275-0.1160.3815-0.2188-0.1349-0.00840.3495-0.0099-0.01730.1770.01280.211482.121743.579333.2336
110.15180.1073-0.03530.0873-0.0202-0.00290.02850.0617-0.17320.1455-0.25230.23510.09240.2668-0.03140.27030.0425-0.02170.2521-0.03830.22283.951736.155336.0427
120.3495-0.0785-0.23480.6596-0.08740.4147-0.0296-0.04180.01990.1785-0.05590.2701-0.1714-0.1472-0.10790.1343-0.00650.00740.2727-0.01480.21563.548226.05117.4408
130.42350.13420.18390.7154-0.07080.2305-0.04830.03830.01460.00090.034-0.0114-0.0531-0.0043-0.10330.1484-0.00330.03820.1433-0.02310.102273.993725.031910.7605
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN C AND (RESSEQ 3:29)
2X-RAY DIFFRACTION2CHAIN C AND (RESSEQ 30:58)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 547:568)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 569:594)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 595:657)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 658:684)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 685:791)
8X-RAY DIFFRACTION8CHAIN D AND (RESSEQ 3:8)
9X-RAY DIFFRACTION9CHAIN D AND (RESSEQ 9:26)
10X-RAY DIFFRACTION10CHAIN D AND (RESSEQ 27:37)
11X-RAY DIFFRACTION11CHAIN D AND (RESSEQ 38:59)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 545:630)
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 631:791)

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