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- PDB-2x56: Yersinia Pestis Plasminogen Activator Pla (Native) -

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Basic information

Entry
Database: PDB / ID: 2x56
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: 2.3 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 / 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 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 13-STRANDED BARREL THIS IS REPRESENTED BY A 14-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COAGULASE/FIBRINOLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,17219
Polymers32,6561
Non-polymers5,51618
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)140.241, 140.241, 130.502
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-2081-

HOH

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Components

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


Mass: 32655.635 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.: 18 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 5.34 Å3/Da / Density % sol: 77 % / Description: NONE
Crystal growpH: 4.8 / Details: 27% PEG 400, 0.1 M LISO4, 0.1 M LI CITRATE, PH 4.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 31644 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 14.2 % / Biso Wilson estimate: 35.36 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 31

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Processing

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

Resolution: 2.3→19.97 Å / SU ML: 0.29 / σ(F): 0.12 / Phase error: 20.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.226 1854 5.9 %
Rwork0.199 --
obs0.201 31644 92.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.24 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.0133 Å20 Å20 Å2
2--3.0133 Å20 Å2
3----6.0265 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2173 0 194 135 2502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072409
X-RAY DIFFRACTIONf_angle_d1.2173188
X-RAY DIFFRACTIONf_dihedral_angle_d21.772899
X-RAY DIFFRACTIONf_chiral_restr0.091306
X-RAY DIFFRACTIONf_plane_restr0.004394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2964-2.35840.23821200.21561959X-RAY DIFFRACTION81
2.3584-2.42770.25431380.21012141X-RAY DIFFRACTION88
2.4277-2.50590.25461340.21722122X-RAY DIFFRACTION87
2.5059-2.59530.24711340.20782133X-RAY DIFFRACTION88
2.5953-2.69890.2131350.19442226X-RAY DIFFRACTION90
2.6989-2.82150.25141350.19122263X-RAY DIFFRACTION93
2.8215-2.96980.23031440.18642247X-RAY DIFFRACTION92
2.9698-3.15520.21821460.17812337X-RAY DIFFRACTION95
3.1552-3.39770.19191480.16842386X-RAY DIFFRACTION97
3.3977-3.73760.19681540.16292441X-RAY DIFFRACTION98
3.7376-4.27380.18751540.18512453X-RAY DIFFRACTION98
4.2738-5.36710.18991490.1752479X-RAY DIFFRACTION97
5.3671-19.96740.26031630.24562603X-RAY DIFFRACTION97
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)
10.1520.2357-0.11290.41130.10760.5413-0.0199-0.0096-0.1178-0.0599-0.0297-0.0740.01640.01540.04290.0839-0.0004-0.00190.10210.02330.0578-15.686758.8349.6027
20.6271-0.06860.29190.31310.04161.3570.012-0.00050.0675-0.05590.008-0.08090.2197-0.0662-0.01230.0543-0.0356-0.0030.11170.04270.0613-14.883658.93977.8329
30.6473-0.0781.05140.62810.02161.7138-0.04170.55160.32610.0749-0.0785-0.06870.08270.77490.11680.06610.007-0.00740.43630.07550.10994.461563.644119.737
41.10440.4136-0.15730.21410.01640.2755-0.04850.20.13180.01120.00560.0299-0.00390.01580.03470.1163-0.0696-0.00180.19510.03610.1339-12.675162.4997.9392
52.48361.21820.19510.89410.41490.2386-0.01650.4659-0.2565-0.08930.0901-0.16550.04370.0211-0.0720.1262-0.064-0.01340.18020.00280.1397-15.843456.73655.6678
62.99770.24870.3810.93320.44990.65540.19410.0995-0.22080.1112-0.2405-0.01090.0919-0.02970.03760.1117-0.053-0.02050.12550.02360.1059-27.51651.484713.1
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 5:53)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 54:134)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 135:161)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 162:216)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 217:280)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 281:292)

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