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- PDB-2x55: Yersinia Pestis Plasminogen Activator Pla (Native) -

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Basic information

Entry
Database: PDB / ID: 2x55
TitleYersinia Pestis Plasminogen Activator Pla (Native)
ComponentsCOAGULASE/FIBRINOLYSIN
KeywordsHYDROLASE / TRANSMEMBRANE / ASPARTYL PROTEASE / CELL OUTER MEMBRANE / OMPTIN / PROTEASE
Function / homology
Function and homology information


plasminogen activator Pla / hemostasis / fibrinolysis / cell outer membrane / aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
OMPT-like / 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 / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Plasminogen activator
Similarity search - Component
Biological speciesYERSINIA PESTIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsEren, E. / Murphy, M. / Goguen, J. / van den Berg, B.
CitationJournal: Structure / Year: 2010
Title: An Active Site Water Network in the Plasminogen Activator Pla from Yersinia Pestis
Authors: Eren, E. / Murphy, M. / Goguen, J. / van den Berg, B.
History
DepositionFeb 5, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Structure summary / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Source and taxonomy / Category: citation_author / entity_src_gen
Item: _citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ... DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COAGULASE/FIBRINOLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,95326
Polymers32,7131
Non-polymers7,24025
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)140.341, 140.341, 130.426
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-2131-

HOH

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Components

#1: Protein COAGULASE/FIBRINOLYSIN / PLASMINOGEN ACTIVATOR / PLA


Mass: 32712.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) YERSINIA PESTIS (bacteria) / Plasmid: PB22 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: P17811, plasminogen activator Pla
#2: Chemical...
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 200 / 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: 5.09 Å3/Da / Density % sol: 75.65 % / Description: NONE
Crystal growpH: 4.8
Details: 27% PEG 400, 0.1 M LISO4, 0.1 M LITHIUM CITRATE, PH 4.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 60190 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Biso Wilson estimate: 24.41 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 46.1
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.6_289)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NATIVE PLA OSMIUM DERIVATIVE

Resolution: 1.85→19.98 Å / SU ML: 0.22 / σ(F): 0.14 / Phase error: 17.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.209 3538 5.9 %
Rwork0.196 --
obs0.196 60269 93.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 78.32 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.5189 Å20 Å20 Å2
2--1.5189 Å20 Å2
3----6.8604 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2177 0 222 200 2599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072434
X-RAY DIFFRACTIONf_angle_d1.243212
X-RAY DIFFRACTIONf_dihedral_angle_d21.136902
X-RAY DIFFRACTIONf_chiral_restr0.1304
X-RAY DIFFRACTIONf_plane_restr0.005396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8509-1.87620.2131070.22951789X-RAY DIFFRACTION74
1.8762-1.9030.20911350.20441954X-RAY DIFFRACTION83
1.903-1.93140.19531290.19232112X-RAY DIFFRACTION88
1.9314-1.96150.19641400.18312117X-RAY DIFFRACTION88
1.9615-1.99370.18841320.16922086X-RAY DIFFRACTION87
1.9937-2.0280.18061400.17062216X-RAY DIFFRACTION92
2.028-2.06480.18891510.16442195X-RAY DIFFRACTION92
2.0648-2.10450.21331330.16882216X-RAY DIFFRACTION92
2.1045-2.14740.17161160.17052211X-RAY DIFFRACTION91
2.1474-2.19410.18731420.17232263X-RAY DIFFRACTION94
2.1941-2.2450.19961390.17382289X-RAY DIFFRACTION95
2.245-2.30110.18561350.1812297X-RAY DIFFRACTION95
2.3011-2.36320.21311390.18492261X-RAY DIFFRACTION94
2.3632-2.43260.22621460.18912282X-RAY DIFFRACTION94
2.4326-2.5110.21431450.2032306X-RAY DIFFRACTION95
2.511-2.60060.19221460.18752282X-RAY DIFFRACTION94
2.6006-2.70450.20691460.19982326X-RAY DIFFRACTION96
2.7045-2.82720.2521430.19742334X-RAY DIFFRACTION96
2.8272-2.97580.21111490.19162337X-RAY DIFFRACTION96
2.9758-3.16160.18931480.18172361X-RAY DIFFRACTION97
3.1616-3.40460.18071500.17632428X-RAY DIFFRACTION98
3.4046-3.74520.18131520.17012462X-RAY DIFFRACTION99
3.7452-4.28250.18281560.19052455X-RAY DIFFRACTION99
4.2825-5.3780.19081550.18482511X-RAY DIFFRACTION99
5.378-19.9820.28231640.26112641X-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)
10.42830.3382-0.33420.17310.02880.3863-0.0324-0.1389-0.0242-0.0727-0.0394-0.0330.06250.0540.07170.0617-0.0262-0.00070.09960.0350.1167-12.198758.695710.0133
21.4991-0.60730.4356-0.01210.09111.04690.11480.09210.1873-0.0654-0.0577-0.07030.16990.0035-0.05130.0761-0.0157-0.01210.10410.04520.1187-12.618160.34199.3035
30.8609-0.04840.8936-0.16390.18012.05340.0412-0.19210.08170.0175-0.0708-0.0210.2291-0.31050.05240.0699-0.0585-0.01630.07780.04770.1044-17.386957.72436.3801
40.01540.4676-0.12440.26530.2011.6012-0.1148-0.05710.13770.01240.051-0.05870.03130.42050.06280.0411-0.0007-0.00960.21820.02580.1026-0.603765.020416.6572
50.76650.4469-0.21210.41090.19750.8204-0.11480.2396-0.0732-0.05930.1234-0.0851-0.02810.01070.01650.1172-0.069-0.00660.16160.02870.1575-14.185360.33295.3284
60.56890.8249-0.18571.1830.02180.584-0.06430.1039-0.2257-0.0710.0061-0.20180.08220.03990.05140.073-0.054-0.00510.14430.01920.0952-20.476354.40839.1473
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 5:53)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 54:94)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 95:134)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 135:177)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 178:232)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 233:293)

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