SAXSdb — 3hw2

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

Protein sifA

Salmonella enterica subsp. enterica serovar Typhimurium

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–336	Not recorded	Pleckstrin homology domain-containing family M member 2 × 1 （Q8IWE5）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；30% PEG 4000, 0.2M Na acetate trihydrate, 0.1 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.30 Å R-free 0.309

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 3HW2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3CXB Crystal Structure of sifa and skip Deposited 2008-04-24	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–336（336 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20% Poly acrylic acid5100, 0.05M magnesium chloride, 0.1M Hepes, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.288

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SIFA_SALTY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–336； UniProt 1–336

Pleckstrin homology domain-containing family M member 2

Homo sapiens

UniProt Q8IWE5

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 771–875	Fragment：Pleskrin homology (PH) domain, UNP residues 771-876	Protein sifA × 1 （Q56061）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；30% PEG 4000, 0.2M Na acetate trihydrate, 0.1 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.30 Å R-free 0.309

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 3HW2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3CXB Crystal Structure of sifa and skip Deposited 2008-04-24	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 773–884（112 aa） Fragment：PH motif, UNP residues 773-884	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20% Poly acrylic acid5100, 0.05M magnesium chloride, 0.1M Hepes, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.288
3ZFW Crystal structure of the TPR domain of kinesin light chain 2 in complex with a tryptophan-acidic cargo peptide Deposited 2012-12-12	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain X 203–212（10 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.10 M MES PH 6.5, 0.2 L-PROLINE, 7% PGA	Resolution 2.90 Å R-free 0.244
3ZFW Crystal structure of the TPR domain of kinesin light chain 2 in complex with a tryptophan-acidic cargo peptide Deposited 2012-12-12	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Y 203–212（10 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.10 M MES PH 6.5, 0.2 L-PROLINE, 7% PGA	Resolution 2.90 Å R-free 0.244
8JCA Cyrstal structure of SKIP RUN domain in complex with GTP-bound Arl8b(Q75L) Deposited 2023-05-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–165（165 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；800mM Potassiam phosphate dibasic 1.2 M Sodium phosphate monobasic 0.1M CAPS/Sodium hydroxide 0.2M Lithium sulfate pH10.5	Resolution 1.65 Å R-free 0.206

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PKHM2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–105； UniProt 771–875

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	3hw2
Deposition date deposition_date	2009-06-17
Structure title title	Crystal structure of the SifA-SKIP(PH) complex
Keywords keywords	sifa, protein complex, salmonella infection, late effector, Virulence, Phosphoprotein, SIGNALING PROTEIN; SIGNALING PROTEIN
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	25.40 Å
Radius of gyration Rg (electron density) rg_electron	24.44 Å
Forward intensity I(0) i0	37821400.00
Molecular weight molecular_weight	47012.0 kDa
Excluded volume excluded_volume	58731 Å³
Envelope volume envelope_volume	75014 Å³
Hydration-shell volume shell_volume	25746 Å³
Envelope diameter envelope_diameter	82.9 Å
Shell Rg shell_rg	31.47 Å
Envelope Rg envelope_rg	24.48 Å
Shape Rg shape_rg	24.46 Å
Total Rg total_rg	25.21 Å
Total atoms total_atoms	3297
Residues n_residues	413
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	80.0 Å
Rg (real space) rg_real	25.31 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	3.7820e+07
I(0) uncertainty (real space) i0_real_error	5.0670e+05
Rg (reciprocal space) rg_reciprocal	25.34 Å
I(0) (reciprocal space) i0_reciprocal	37820000.0000
Solution quality estimate total_estimate	0.7519
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.2 Å
Skewness Skewness skewness	0.160
Kurtosis Kurtosis kurtosis	-0.586
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7600000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.946; Stabil: 1.000; Sysdev: 0.315; Positv: 1.000; Valcen: 1.000; Smooth: 0.988

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Protein sifA
Molecular weight formula_weight	38546.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3297

MPITIGNGFLKSEILTNSPRNTKEAWWKVLWEKIKDFFFSTGKAKADRCLHEMLFAERAPTRERLTEIFFELKELACASQRDRFQVHNPHENDATIILRIMDQNEENELLRITQNTDTFSCEVMGNLYFLMKDRPDILKSHPQMTAMIKRRYSEIVDYPLPSTLCLNPAGAPILSVPLDNIEGYLYTELRKGHLDGWKAQEKATYLAAKIQSGIEKTTRILHHANISESTQQNAFLETMAMCGLKQLEIPPPHTHIPIEKMVKEVLLADKTFQAFLVTDPSTSQSMLAEIVEAISDQVFHAIFRIDPQAIQKMAEEQLTTLHVRSEQQSGCLCCFL

来源 Source

来源生物 organism	Salmonella enterica subsp. enterica serovar Typhimurium
NCBI Class编号 ncbi_taxonomy_id	99287
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Pleckstrin homology domain-containing family M member 2
Molecular weight formula_weight	11734.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

TITKEGMLHYKAGTSYLGKEHWKTCFVVLSNGILYQYPDRTDVIPLLSVNMGGEQCGGCRRANTTDRPHAFQVILSDRPCLELSAESEAEMAEWMQHLCQAVSKG

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3hw2A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2440 — Secreted effector protein SifA fold
Homologous superfamily homologous superfamily	10 — Secreted effector protein SifA

Domain ID domain_id	3hw2A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	390 — Enolase-like; domain 1
Homologous superfamily homologous superfamily	70 — Salmonella typhimurium protein

Domain ID domain_id	3hw2A03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1740 — Rna Polymerase Sigma Factor; Chain: A
Homologous superfamily homologous superfamily	30 — Secreted effector protein SifA helical domain

Domain ID domain_id	3hw2B00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

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8. Citations (1)

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Unit-cell length a length_a	91.799 Å
Unit-cell length b length_b	110.866 Å
Unit-cell length c length_c	44.274 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2473
R_work r_work	0.2404
R_free r_free	0.3093

fit	/app/data/saxs_computation/hw/3hw2/3hw2.fit
pddf	/app/data/pr_computation/hw/3hw2/3hw2.pr.out
profile	/app/data/saxs_computation/hw/3hw2/3hw2.dat

Crystal structure of the SifA-SKIP(PH) complex

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

Protein sifA

State in the Current Structure

Other States of the Same Protein in the Database

Pleckstrin homology domain-containing family M member 2

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)