SAXSdb — 8q52

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

Leucine-specific-binding protein,Chemotaxis protein CheY

Escherichia coli K-12

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 24–163 Chain A； UniProt 273–351	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；30% PEG 4000, 0.1M Tris.HCl, 0.3M Li sulfate	Resolution 2.15 Å R-free 0.253

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 8Q52	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1USG L-leucine-binding protein, apo form Deposited 2003-11-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 24–369（346 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；PEG 5000, SODIUM ACETATE PH 4.6, AMMONIUM SULPHATE, COCL2.	Resolution 1.53 Å R-free 0.216
1USI L-leucine-binding protein with phenylalanine bound Deposited 2003-11-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–369（346 aa）	Not recorded	PHE PHENYLALANINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 1.80 Å R-free 0.222
1USI L-leucine-binding protein with phenylalanine bound Deposited 2003-11-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 24–369（346 aa）	Not recorded	PHE PHENYLALANINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 1.80 Å R-free 0.222
1USK L-leucine-binding protein with leucine bound Deposited 2003-11-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–369（346 aa）	Not recorded	LEU LEUCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；PEG 4000, SODIUM CITRATE, PH 5.6, 2-PROPANOL	Resolution 2.00 Å R-free 0.252
1USK L-leucine-binding protein with leucine bound Deposited 2003-11-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 24–369（346 aa）	Not recorded	LEU LEUCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；PEG 4000, SODIUM CITRATE, PH 5.6, 2-PROPANOL	Resolution 2.00 Å R-free 0.252
1USK L-leucine-binding protein with leucine bound Deposited 2003-11-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 24–369（346 aa）	Not recorded	LEU LEUCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；PEG 4000, SODIUM CITRATE, PH 5.6, 2-PROPANOL	Resolution 2.00 Å R-free 0.252
1USK L-leucine-binding protein with leucine bound Deposited 2003-11-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 24–369（346 aa）	Not recorded	LEU LEUCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；PEG 4000, SODIUM CITRATE, PH 5.6, 2-PROPANOL	Resolution 2.00 Å R-free 0.252
2LBP STRUCTURE OF THE L-LEUCINE-BINDING PROTEIN REFINED AT 2.4 ANGSTROMS RESOLUTION AND COMPARISON WITH THE LEU(SLASH)ILE(SLASH)VAL-BINDING PROTEIN STRUCTURE Deposited 1989-04-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 24–369（346 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å

4 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LIVK_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–141； UniProt 24–163 Author chain A； PDBConstruct 243–321； UniProt 273–351

Leucine-specific-binding protein,Chemotaxis protein CheY

Escherichia coli K-12

UniProt Q56312

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 5–105	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；30% PEG 4000, 0.1M Tris.HCl, 0.3M Li sulfate	Resolution 2.15 Å R-free 0.253

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 8Q52	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1TMY CHEY FROM THERMOTOGA MARITIMA (APO-I) Deposited 1997-05-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；PROTEIN WAS CRYSTALLIZED FROM 0.1M TRIS BUFFER (PH 8.5) AND 1.8M AMMONIUM PHOSPHATE	Resolution 1.90 Å
1U0S Chemotaxis kinase CheA P2 domain in complex with response regulator CheY from the thermophile thermotoga maritima Deposited 2004-07-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Y 2–119（118 aa） Fragment：response regulatory domain, CheY response regulator	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；25-30% PEG 12K, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.90 Å R-free 0.253
2LLE Computational design of an eight-stranded (beta/alpha)-barrel from fragments of different folds Deposited 2011-11-07	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–11（11 aa） Chain A 34–103（70 aa）	Mutation：R4I, D78G, I95L, L201A,V213G Mutation：R4I, D78G, I95L, L201A,V213G	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.5；313 K；Ionic strength (raw mmCIF value) 350；Pressure ambient NMR sample composition 0.5 mM [U-100% 15N] CheYHisF-sfr_RM, 50 mM potassium phosphate, 300 mM potassium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] CheYHisF-sfr_RM, 50 mM potassium phosphate, 300 mM potassium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2TMY CHEY FROM THERMOTOGA MARITIMA (APO-II) Deposited 1997-05-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；0.2M AMMONIUM SULFATE, 0.1M ACETATE BUFFER (PH 4.6), 30% PEG 4000, 15MM MGCL2	Resolution 2.30 Å
3TMY CHEY FROM THERMOTOGA MARITIMA (MN-III) Deposited 1997-06-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Not recorded	MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；0.2M AMMONIUM SULFATE, 0.1M HEPES BUFFER (PH 7.0), 25% PEG 4000, 15MM MANGANESE CHLORIDE	Resolution 2.20 Å
3TMY CHEY FROM THERMOTOGA MARITIMA (MN-III) Deposited 1997-06-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–120（120 aa）	Not recorded	MN MANGANESE (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；0.2M AMMONIUM SULFATE, 0.1M HEPES BUFFER (PH 7.0), 25% PEG 4000, 15MM MANGANESE CHLORIDE	Resolution 2.20 Å
4IGA The crystal structure of an activated Thermotoga maritima CheY with N-terminal region of FliM Deposited 2012-12-17	Different construct 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 1–120（120 aa）	Not recorded	MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30% (w/v) PEG 4000, 0.1M TRIS pH 8.5, 0.2M sodium acetate, 0.2M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.73 Å R-free 0.276
4QYW Structure of phosphono-CheY from T.maritima Deposited 2014-07-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–120（119 aa）	Mutation：D54(CYQ), C81A Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；100mM acetate, pH 5.5, 350 uM Sc(ClO4)3, 0.02% azide, 150 mM sodium malonate, 19% PeEG 6000., VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.268
4TMY CHEY FROM THERMOTOGA MARITIMA (MG-IV) Deposited 1997-06-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–120（120 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；0.2M AMMONIUM SULFATE, 0.1M HEPES BUFFER (PH 7.0), 25% PEG 4000, 15MM MAGNESIUM CHLORIDE	Resolution 2.80 Å
4TMY CHEY FROM THERMOTOGA MARITIMA (MG-IV) Deposited 1997-06-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–120（120 aa）	Not recorded	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；0.2M AMMONIUM SULFATE, 0.1M HEPES BUFFER (PH 7.0), 25% PEG 4000, 15MM MAGNESIUM CHLORIDE	Resolution 2.80 Å
6C40 CheY41PyTyrD54K from Thermotoga maritima Deposited 2018-01-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 2–119（118 aa） Chain D 2–119（118 aa）	Mutation：E41PyTyr, D54K Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：E41PyTyr, D54K Non-standard monomer：Yes (specific site not provided by mmCIF)	CU COPPER (II) ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；HEPES pH 7, ammonium sulfate, PEG 4000	Resolution 2.70 Å R-free 0.295

9 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CHEY_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 142–242； UniProt 5–105

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	8q52
Deposition date deposition_date	2023-08-08
Structure title title	A PBP-like protein built from fragments of different folds
Keywords keywords	;Protein fold evolution, gene duplication, flavodoxin-like fold, periplasmic-binding protein-like I fold, sub-domain, chimeric proteins, homology, DE NOVO PROTEIN ;; DE NOVO 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	21.25 Å
Radius of gyration Rg (electron density) rg_electron	20.35 Å
Forward intensity I(0) i0	21347500.00
Molecular weight molecular_weight	34647.0 kDa
Excluded volume excluded_volume	43232 Å³
Envelope volume envelope_volume	50275 Å³
Hydration-shell volume shell_volume	20970 Å³
Envelope diameter envelope_diameter	72.1 Å
Shell Rg shell_rg	26.56 Å
Envelope Rg envelope_rg	20.49 Å
Shape Rg shape_rg	20.33 Å
Total Rg total_rg	21.22 Å
Total atoms total_atoms	2420
Residues n_residues	320
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	68.8 Å
Rg (real space) rg_real	21.23 Å
Rg uncertainty (real space) rg_real_error	0.50 Å
I(0) (real space) i0_real	2.1350e+07
I(0) uncertainty (real space) i0_real_error	2.6970e+05
Rg (reciprocal space) rg_reciprocal	21.23 Å
I(0) (reciprocal space) i0_reciprocal	21350000.0000
Solution quality estimate total_estimate	0.8119
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.3 Å
Skewness Skewness skewness	0.361
Kurtosis Kurtosis kurtosis	-0.241
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4961000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.852; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Leucine-specific-binding protein,Chemotaxis protein CheY
Molecular weight formula_weight	34554.6 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	2599

MDDIKVAVVGAMSGPIAQWGDMEFNGARQAIKDINAKGGIKGDKLVGVEYDDACDPKQAVAVANKIVNDGIKYVIGHLCSSSTQPASDIYEDEGILMISPGATNPELTQRGYQHIMRTAGLDSSQGPTAAKYILETVKPQRVLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPKRYDQDPANQGIVDALKADKKDPSGPYVWITYAAVQSLATALERTGSDEPLALVKDLKANGANTVIGPLNWDEKGDLKG

来源 Source

来源生物 organism	Escherichia coli K-12
NCBI Class编号 ncbi_taxonomy_id	83333
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	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	168

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8. Citations (1)

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Unit-cell length a length_a	129.560 Å
Unit-cell length b length_b	129.560 Å
Unit-cell length c length_c	43.640 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	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	tetragonal

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	41.360 Å
R factor r_factor	0.2028
R_work r_work	0.2003
R_free r_free	0.2528

fit	/app/data/saxs_computation/q5/8q52/8q52.fit
pddf	/app/data/pr_computation/q5/8q52/8q52.pr.out
profile	/app/data/saxs_computation/q5/8q52/8q52.dat

A PBP-like protein built from fragments of different folds

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

Leucine-specific-binding protein,Chemotaxis protein CheY

State in the Current Structure

Other States of the Same Protein in the Database

Leucine-specific-binding protein,Chemotaxis protein CheY

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)