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- PDB-2x4m: Yersinia Pestis Plasminogen Activator Pla -

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Basic information

Entry
Database: PDB / ID: 2x4m
TitleYersinia Pestis Plasminogen Activator Pla
ComponentsCOAGULASE/FIBRINOLYSIN
KeywordsHYDROLASE / OMPTIN / TRANSMEMBRANE / ASPARTYL PROTEASE / CELL OUTER MEMBRANE / PROTEASE
Function / homology
Function and homology information


plasminogen activator Pla / 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: 2.55 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 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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. THE SHEETS PRESENTED AS "AB IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 14-STRANDED BARREL THIS IS REPRESENTED BY A 15-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" 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. THE SHEETS PRESENTED AS "BB IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 14-STRANDED BARREL THIS IS REPRESENTED BY A 15-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CA" 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. THE SHEETS PRESENTED AS "CB IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 14-STRANDED BARREL THIS IS REPRESENTED BY A 15-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "DA" 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. THE SHEETS PRESENTED AS "DB IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 14-STRANDED BARREL THIS IS REPRESENTED BY A 15-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
B: COAGULASE/FIBRINOLYSIN
C: COAGULASE/FIBRINOLYSIN
D: COAGULASE/FIBRINOLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,31541
Polymers131,8164
Non-polymers6,50037
Water2,162120
1
A: COAGULASE/FIBRINOLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,96611
Polymers32,9541
Non-polymers2,01310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: COAGULASE/FIBRINOLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3549
Polymers32,9541
Non-polymers1,4008
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: COAGULASE/FIBRINOLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,45010
Polymers32,9541
Non-polymers1,4969
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: COAGULASE/FIBRINOLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,54611
Polymers32,9541
Non-polymers1,59210
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.913, 127.824, 107.175
Angle α, β, γ (deg.)90.00, 90.06, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 15:20 OR RESSEQ 23:32 OR RESSEQ...
211CHAIN B AND (RESSEQ 15:20 OR RESSEQ 23:32 OR RESSEQ...
311CHAIN C AND (RESSEQ 15:20 OR RESSEQ 23:32 OR RESSEQ...
411CHAIN D AND (RESSEQ 15:20 OR RESSEQ 23:32 OR RESSEQ...

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Components

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


Mass: 32953.934 Da / Num. of mol.: 4 / Mutation: YES
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 106 TO ALA ENGINEERED RESIDUE IN CHAIN B, ASP 106 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, ASP 106 TO ALA ENGINEERED RESIDUE IN CHAIN B, ASP 106 TO ALA ENGINEERED RESIDUE IN CHAIN C, ASP 106 TO ALA ENGINEERED RESIDUE IN CHAIN D, ASP 106 TO ALA

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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: 3.63 Å3/Da / Density % sol: 66.16 % / Description: NONE
Crystal growpH: 3.5 / Details: 16% PEG 400, 0.1M LITHIUM CITRATE PH: 3.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.321
ReflectionResolution: 2.55→40 Å / Num. obs: 56736 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.1
Reflection shellResolution: 2.54→2.58 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.93 / % possible all: 79.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→19.93 Å / σ(F): 0.08 / Phase error: 36.38 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.246 1979 3.5 %
Rwork0.185 --
obs0.186 56736 92.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.03 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--17.574 Å20 Å21.1632 Å2
2--4.3517 Å20 Å2
3---11.5647 Å2
Refinement stepCycle: LAST / Resolution: 2.55→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9114 0 248 120 9482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089565
X-RAY DIFFRACTIONf_angle_d1.26712916
X-RAY DIFFRACTIONf_dihedral_angle_d21.53268
X-RAY DIFFRACTIONf_chiral_restr0.0821270
X-RAY DIFFRACTIONf_plane_restr0.0041661
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1070X-RAY DIFFRACTIONPOSITIONAL
12B1070X-RAY DIFFRACTIONPOSITIONAL0.043
13C1070X-RAY DIFFRACTIONPOSITIONAL0.061
14D1070X-RAY DIFFRACTIONPOSITIONAL0.039
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5502-2.6190.29741080.30233201X-RAY DIFFRACTION68
2.619-2.69590.35021270.28633563X-RAY DIFFRACTION76
2.6959-2.78270.29251340.27513845X-RAY DIFFRACTION82
2.7827-2.88180.31181330.26934089X-RAY DIFFRACTION88
2.8818-2.99680.31951490.24354233X-RAY DIFFRACTION91
2.9968-3.13260.28391550.22764342X-RAY DIFFRACTION92
3.1326-3.2970.2561530.20374394X-RAY DIFFRACTION93
3.297-3.50240.26191550.18394417X-RAY DIFFRACTION94
3.5024-3.77090.22041540.16934455X-RAY DIFFRACTION95
3.7709-4.14690.22541580.16694506X-RAY DIFFRACTION96
4.1469-4.7390.20091640.13454564X-RAY DIFFRACTION96
4.739-5.94090.21491580.15334562X-RAY DIFFRACTION97
5.9409-19.1490.26571630.17544627X-RAY DIFFRACTION97

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