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- PDB-4dcb: Y. pestis Plasminogen Activator Pla in Complex with Human Plasmin... -

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Basic information

Entry
Database: PDB / ID: 4dcb
TitleY. pestis Plasminogen Activator Pla in Complex with Human Plasminogen Activation Loop Peptide ALP11
Components
  • Coagulase/fibrinolysin
  • Plasminogen
KeywordsHYDROLASE / Beta barrel / Plasminogen activator / Protease / Outer membrane
Function / homology
Function and homology information


plasminogen activator Pla / 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 ...plasminogen activator Pla / 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 / cell outer membrane / 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 / collagen-containing extracellular matrix / endopeptidase activity / protease binding / aspartic-type endopeptidase activity / blood microparticle / negative regulation of cell population proliferation / protein domain specific binding / 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
Aspartyl proteases, omptin family signature 2. / Peptidase A26, omptin / Peptidase A26, omptin, conserved site / Omptin family / Aspartyl proteases, omptin family signature 1. / Outer membrane adhesin/peptidase omptin / Peptidase S1A, plasmin / divergent subfamily of APPLE domains / PAN/Apple domain profile. / PAN domain ...Aspartyl proteases, omptin family signature 2. / Peptidase A26, omptin / Peptidase A26, omptin, conserved site / Omptin family / Aspartyl proteases, omptin family signature 1. / Outer membrane adhesin/peptidase omptin / Peptidase S1A, plasmin / divergent subfamily of APPLE domains / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
PHOSPHATE ION / Plasminogen / Plasminogen activator
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.033 Å
AuthorsEren, E. / van den Berg, B.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural basis for activation of an integral membrane protease by lipopolysaccharide.
Authors: Eren, E. / van den Berg, B.
History
DepositionJan 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Jul 7, 2021Group: Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_sheet_hbond ...pdbx_database_status / pdbx_struct_sheet_hbond / struct_conf / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site
Item: _pdbx_database_status.pdb_format_compatible / _struct_conf.pdbx_PDB_helix_id ..._pdbx_database_status.pdb_format_compatible / _struct_conf.pdbx_PDB_helix_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Coagulase/fibrinolysin
F: Plasminogen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,49810
Polymers34,3882
Non-polymers1,1108
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-59 kcal/mol
Surface area14790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.377, 63.105, 201.225
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AF

#1: Protein Coagulase/fibrinolysin / Plasminogen activator


Mass: 33281.316 Da / Num. of mol.: 1 / Mutation: D84N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: pla, YPPCP1.07, YP_pPCP08 / Plasmid: pB22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)T1 / References: UniProt: P17811, plasminogen activator Pla
#2: Protein/peptide Plasminogen / Plasmin heavy chain A / Activation peptide / Angiostatin / Plasmin heavy chain A / short form / ...Plasmin heavy chain A / Activation peptide / Angiostatin / Plasmin heavy chain A / short form / Plasmin light chain B


Mass: 1106.386 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This seqeunce naturally exists in human plasminogen activation domain
Source: (synth.) Homo sapiens (human) / References: UniProt: P00747, plasmin

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Non-polymers , 5 types, 114 molecules

#3: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.42 Å3/Da / Density % sol: 49.12 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.5
Details: 45% (v/v) 2-methyl-2,4-pentanediol (MPD), 0.2 M NH4KH2PO4 and 0.1M NaOAc, pH 5.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.972 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 9, 2010
RadiationMonochromator: channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 21867 / % possible obs: 99.8 % / Redundancy: 5.5 % / Rsym value: 0.101 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Rsym valueDiffraction-ID% possible all
2.03-2.075.10.427199.7
2.07-2.15.40.411199.6
2.1-2.145.50.379199.7
2.14-2.195.40.3491100
2.19-2.235.40.334199.9
2.23-2.295.40.304199.4
2.29-2.345.40.287199.8
2.34-2.415.40.273199.8
2.41-2.485.40.251100
2.48-2.565.50.242199.9
2.56-2.655.50.2071100
2.65-2.765.60.171100
2.76-2.885.60.1481100
2.88-3.035.70.1171100
3.03-3.225.80.091100
3.22-3.475.80.072199.9
3.47-3.825.80.062199.9
3.82-4.375.80.058199.9
4.37-5.515.70.061199.8
5.51-505.30.068198.2

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X55

2x55


Resolution: 2.033→19.759 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.23 / σ(F): 0 / Phase error: 20.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2319 1917 9.14 %
Rwork0.1804 --
obs0.1849 20964 95.52 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.691 Å2 / ksol: 0.349 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.9586 Å2-0 Å2-0 Å2
2---1.0187 Å20 Å2
3----3.94 Å2
Refinement stepCycle: LAST / Resolution: 2.033→19.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2267 0 74 106 2447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082394
X-RAY DIFFRACTIONf_angle_d1.1563238
X-RAY DIFFRACTIONf_dihedral_angle_d16.024843
X-RAY DIFFRACTIONf_chiral_restr0.085324
X-RAY DIFFRACTIONf_plane_restr0.004411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0335-2.10610.23151740.16931742X-RAY DIFFRACTION89
2.1061-2.19030.23231790.1761813X-RAY DIFFRACTION92
2.1903-2.28980.25211820.17311803X-RAY DIFFRACTION92
2.2898-2.41040.23851890.18371876X-RAY DIFFRACTION95
2.4104-2.56110.25411880.18521865X-RAY DIFFRACTION95
2.5611-2.75830.23561940.18051926X-RAY DIFFRACTION97
2.7583-3.0350.25281950.18281934X-RAY DIFFRACTION97
3.035-3.47210.20612000.1761973X-RAY DIFFRACTION99
3.4721-4.36670.21452040.16752022X-RAY DIFFRACTION99
4.3667-19.76010.2422120.19652093X-RAY DIFFRACTION99
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)
10.6745-0.17310.41040.54980.66331.381-0.01830.01860.0807-0.0411-0.0401-0.0481-0.01680.01020.03820.0392-0.0169-0.01940.04340.03170.1206-11.451313.897742.3937
20.6594-0.1680.0290.92980.5180.37860.03120.25310.0313-0.2379-0.0689-0.0213-0.0477-0.05180.04320.13450.01030.00950.1409-0.00650.0667-13.665812.542728.4439
30.83060.4112-0.31930.7772-0.29391.34140.01170.06630.04140.175-0.081-0.0768-0.0264-0.04110.05850.0754-0.0361-0.00540.0663-0.00290.185-19.680123.11955.887
41.3818-0.1643-0.36161.11940.07020.0657-0.01240.5753-0.0574-0.3576-0.0459-0.09990.33750.17150.030.27840.02210.02390.3078-0.04670.0308-10.43066.853916.5737
50.37480.3104-0.45930.349-0.621.6171-0.07120.0045-0.15590.1026-0.0981-0.2268-0.1660.03930.11540.0549-0.0085-0.01460.05230.00950.1242-21.164916.4851.8228
60.9139-0.17350.67151.646-0.52650.8442-0.00180.35270.0701-0.3525-0.1555-0.0011-0.30110.22840.08270.0845-0.05810.0250.15660.08020.0537-9.621519.628425.712
70.37030.2054-0.2040.40130.22760.32530.03520.0912-0.06780.0424-0.00280.16760.02050.0287-0.00750.03-0.0148-0.00220.0622-0.0220.1224-20.00459.990447.1031
80.46410.1240.30830.6068-0.38850.6053-0.17150.76210.2117-0.58440.0784-0.15950.07780.2290.18320.6755-0.2210.03190.54470.26110.2903-6.06323.8217.0167
90.54640.09450.36230.32290.02081.4584-0.04860.0484-0.0149-0.02640.0780.0007-0.0167-0.0574-0.00610.0679-0.0068-0.0160.0826-0.01190.095-15.019810.258842.2218
100.78920.2826-0.44820.80650.00550.29030.01290.89770.1106-0.90530.1818-0.03880.38890.4558-0.2170.59720.01690.06530.59930.06880.0482-9.340812.87334.8251
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 5:33)
2X-RAY DIFFRACTION2(chain A and resid 34:117)
3X-RAY DIFFRACTION3(chain A and resid 118:134)
4X-RAY DIFFRACTION4(chain A and resid 135:172)
5X-RAY DIFFRACTION5(chain A and resid 173:192)
6X-RAY DIFFRACTION6(chain A and resid 193:226)
7X-RAY DIFFRACTION7(chain A and resid 227:252)
8X-RAY DIFFRACTION8(chain A and resid 253:273)
9X-RAY DIFFRACTION9(chain A and resid 274:293)
10X-RAY DIFFRACTION10(chain F and resid 557:567)

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