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2x55

Yersinia Pestis Plasminogen Activator Pla (Native)

Method: X-RAY DIFFRACTION Dmax: 77.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

COAGULASE/FIBRINOLYSIN

YERSINIA PESTIS

UniProt P17811

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 21–312 Not recorded C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 23 SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.8；27% PEG 400, 0.1 M LISO4, 0.1 M LITHIUM CITRATE, PH 4.8 Resolution 1.85 Å R-free 0.209

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 2X55 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2X4M Yersinia Pestis Plasminogen Activator Pla Deposited 2010-02-05 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–312（292 aa）
Mutation：YES SO4 SULFATE ION × 5 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 5 X-RAY DIFFRACTION
X-ray crystallization conditions pH 3.5；16% PEG 400, 0.1M LITHIUM CITRATE PH: 3.5
Resolution 2.55 Å R-free 0.246
2X4M Yersinia Pestis Plasminogen Activator Pla Deposited 2010-02-05 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 21–312（292 aa）
Mutation：YES SO4 SULFATE ION × 5 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 3.5；16% PEG 400, 0.1M LITHIUM CITRATE PH: 3.5
Resolution 2.55 Å R-free 0.246
2X4M Yersinia Pestis Plasminogen Activator Pla Deposited 2010-02-05 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 21–312（292 aa）
Mutation：YES SO4 SULFATE ION × 6 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 3.5；16% PEG 400, 0.1M LITHIUM CITRATE PH: 3.5
Resolution 2.55 Å R-free 0.246
2X4M Yersinia Pestis Plasminogen Activator Pla Deposited 2010-02-05 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 21–312（292 aa）
Mutation：YES SO4 SULFATE ION × 7 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 3.5；16% PEG 400, 0.1M LITHIUM CITRATE PH: 3.5
Resolution 2.55 Å R-free 0.246
2X56 Yersinia Pestis Plasminogen Activator Pla (Native) Deposited 2010-02-05 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–312（292 aa）
Not recorded C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 18 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.8；27% PEG 400, 0.1 M LISO4, 0.1 M LI CITRATE, PH 4.8
Resolution 2.30 Å R-free 0.226
4DCB Y. pestis Plasminogen Activator Pla in Complex with Human Plasminogen Activation Loop Peptide ALP11 Deposited 2012-01-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 25–312（288 aa）
Mutation：D84N MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；45% (v/v) 2-methyl-2,4-pentanediol (MPD), 0.2 M NH4KH2PO4 and 0.1M NaOAc, pH 5.5, VAPOR DIFFUSION, HANGING DROP
Resolution 2.03 Å R-free 0.232

3 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name COLY_YERPE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–292； UniProt 21–312

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 2x55

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2x55
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2x55
Deposition date deposition_date2010-02-05
Structure title titleYersinia Pestis Plasminogen Activator Pla (Native)
Keywords keywordsTRANSMEMBRANE, ASPARTYL PROTEASE, CELL OUTER MEMBRANE, OMPTIN, PROTEASE, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier22.59 Å
Radius of gyration Rg (electron density) rg_electron22.08 Å
Forward intensity I(0) i017707800.00
Molecular weight molecular_weight33969.0 kDa
Excluded volume excluded_volume43397 ų
Envelope volume envelope_volume50333 ų
Hydration-shell volume shell_volume20096 ų
Envelope diameter envelope_diameter79.5 Å
Shell Rg shell_rg28.01 Å
Envelope Rg envelope_rg22.52 Å
Shape Rg shape_rg22.08 Å
Total Rg total_rg22.92 Å
Total atoms total_atoms2399
Residues n_residues274
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax77.9 Å
Rg (real space) rg_real22.80 Å
Rg uncertainty (real space) rg_real_error0.64 Å
I(0) (real space) i0_real1.7710e+07
I(0) uncertainty (real space) i0_real_error2.5460e+05
Rg (reciprocal space) rg_reciprocal22.75 Å
I(0) (reciprocal space) i0_reciprocal17710000.0000
Solution quality estimate total_estimate0.8318
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.2 Å
Skewness Skewness skewness0.573
Kurtosis Kurtosis kurtosis-0.240
Angular range angular_range— – 0.3500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3677000.0000
Real-space data points n_real_points67
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.707; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.782; Smooth: 0.905
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2x55a1
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.4 — Transmembrane beta-barrels
Superfamily Superfamily superfamilyf.4.4 — OMPT-like
Family Family familyf.4.4.0 — automated matches
Domain ID domain_idd2x55a2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id2x55A00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily90 — OMPT-like
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8. Citations (1)

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9. Files and Curves (10)