SAXSdb — 2x4m

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1. Protein Identity and Related Structures Protein Identity & Related Structures

COAGULASE/FIBRINOLYSIN

YERSINIA PESTIS

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	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 21–312	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
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 21–312	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
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 21–312	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

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 2X4M	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2X55 Yersinia Pestis Plasminogen Activator Pla (Native) 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）	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
2X56 Yersinia Pestis Plasminogen Activator Pla (Native) 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）	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 3 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 Author chain B； PDBConstruct 1–292； UniProt 21–312 Author chain C； PDBConstruct 1–292； UniProt 21–312 Author chain D； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2x4m
Deposition date deposition_date	2010-02-05
Structure title title	Yersinia Pestis Plasminogen Activator Pla
Keywords keywords	OMPTIN, TRANSMEMBRANE, ASPARTYL PROTEASE, CELL OUTER MEMBRANE, PROTEASE, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	42.36 Å
Radius of gyration Rg (electron density) rg_electron	41.87 Å
Forward intensity I(0) i0	289320000.00
Molecular weight molecular_weight	132880.0 kDa
Excluded volume excluded_volume	163300 Å³
Envelope volume envelope_volume	227650 Å³
Hydration-shell volume shell_volume	47378 Å³
Envelope diameter envelope_diameter	139.3 Å
Shell Rg shell_rg	44.81 Å
Envelope Rg envelope_rg	40.95 Å
Shape Rg shape_rg	41.84 Å
Total Rg total_rg	42.11 Å
Total atoms total_atoms	9362
Residues n_residues	1163
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	134.9 Å
Rg (real space) rg_real	42.47 Å
Rg uncertainty (real space) rg_real_error	1.22 Å
I(0) (real space) i0_real	2.8930e+08
I(0) uncertainty (real space) i0_real_error	5.1350e+06
Rg (reciprocal space) rg_reciprocal	42.36 Å
I(0) (reciprocal space) i0_reciprocal	289300000.0000
Solution quality estimate total_estimate	0.8687
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	47.4 Å
Skewness Skewness skewness	0.288
Kurtosis Kurtosis kurtosis	-0.701
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9104000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.953; Smooth: 0.565

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	COAGULASE/FIBRINOLYSIN
Molecular weight formula_weight	32953.9 kDa
EC 编号 ec_number	3.4.23.48
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	9482

ASSQLIPNISPDSFTVAASTGMLSGKSHEMLYDAETGRKISQLDWKIKNVAILKGDISWDPYSFLTLNARGWTSLASGSGNMDDYAWMNENQSEWTDHSSHPATNVNHANEYDLNVKGWLLQDENYKAGITAGYQETRFSWTATGGSYSYNNGAYTGNFPKGVRVIGYNQRFSMPYIGLAGQYRINDFELNALFKFSDWVRAHDNDEHYMRDLTFREKTSGSRYYGTVINAGYYVTPNAKVFAEFTYSKYDEGKGGTQTIDKNSGDSVSIGGDAAGISNKNYTVTAGLQYRFGGGGGG

来源 Source

来源生物 organism	YERSINIA PESTIS
NCBI Class编号 ncbi_taxonomy_id	632
宿主生物 host_organism	ESCHERICHIA COLI BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	23

Entity 3 Entity 3 non-polymer

Description description	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
Molecular weight formula_weight	306.4 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	120

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2x4ma1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.4 — Transmembrane beta-barrels
Superfamily Superfamily superfamily	f.4.4 — OMPT-like
Family Family family	f.4.4.0 — automated matches

Domain ID domain_id	d2x4ma2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2x4mb1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.4 — Transmembrane beta-barrels
Superfamily Superfamily superfamily	f.4.4 — OMPT-like
Family Family family	f.4.4.0 — automated matches

Domain ID domain_id	d2x4mb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2x4mc1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.4 — Transmembrane beta-barrels
Superfamily Superfamily superfamily	f.4.4 — OMPT-like
Family Family family	f.4.4.0 — automated matches

Domain ID domain_id	d2x4mc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2x4md1
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.4 — Transmembrane beta-barrels
Superfamily Superfamily superfamily	f.4.4 — OMPT-like
Family Family family	f.4.4.0 — automated matches

Domain ID domain_id	d2x4md2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	2x4mA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	90 — OMPT-like

Domain ID domain_id	2x4mB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	90 — OMPT-like

Domain ID domain_id	2x4mC00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	90 — OMPT-like

Domain ID domain_id	2x4mD00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	90 — OMPT-like

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8. Citations (1)

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Unit-cell length a length_a	69.913 Å
Unit-cell length b length_b	127.824 Å
Unit-cell length c length_c	107.175 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.06 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.550 Å
Low-resolution limit resolution_low	19.930 Å
R factor r_factor	0.1860
R_work r_work	0.1850
R_free r_free	0.2460

fit	/app/data/saxs_computation/x4/2x4m/2x4m.fit
pddf	/app/data/pr_computation/x4/2x4m/2x4m.pr.out
profile	/app/data/saxs_computation/x4/2x4m/2x4m.dat

Yersinia Pestis Plasminogen Activator Pla

1. Protein Identity and Related Structures Protein Identity & Related Structures

COAGULASE/FIBRINOLYSIN

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction