SAXSdb — 3tmy

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

CHEY PROTEIN

Thermotoga maritima

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 1–120	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–120	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

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 3TMY	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 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 oligomeric state 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 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
4IGA The crystal structure of an activated Thermotoga maritima CheY with N-terminal region of FliM Deposited 2012-12-17	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 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 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 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
8Q52 A PBP-like protein built from fragments of different folds Deposited 2023-08-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 5–105（101 aa）	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

9 other PDB entries and 10 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 1–120； UniProt 1–120 Author chain B； PDBConstruct 1–120； UniProt 1–120

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	3tmy
Deposition date deposition_date	1997-06-04
Structure title title	CHEY FROM THERMOTOGA MARITIMA (MN-III)
Keywords keywords	CHEMOTAXIS, PHOSPHORYL TRANSFER, SIGNAL TRANSDUCTION, MANGANESE BINDING; CHEMOTAXIS
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	21.28 Å
Radius of gyration Rg (electron density) rg_electron	20.96 Å
Forward intensity I(0) i0	11414800.00
Molecular weight molecular_weight	25991.0 kDa
Excluded volume excluded_volume	32924 Å³
Envelope volume envelope_volume	39212 Å³
Hydration-shell volume shell_volume	16422 Å³
Envelope diameter envelope_diameter	69.0 Å
Shell Rg shell_rg	26.02 Å
Envelope Rg envelope_rg	21.02 Å
Shape Rg shape_rg	21.00 Å
Total Rg total_rg	21.59 Å
Total atoms total_atoms	1802
Residues n_residues	236
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	71.6 Å
Rg (real space) rg_real	21.42 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	1.1410e+07
I(0) uncertainty (real space) i0_real_error	1.6170e+05
Rg (reciprocal space) rg_reciprocal	21.40 Å
I(0) (reciprocal space) i0_reciprocal	11410000.0000
Solution quality estimate total_estimate	0.6594
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.1 Å
Skewness Skewness skewness	0.475
Kurtosis Kurtosis kurtosis	-0.442
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6844000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.694; Stabil: 1.000; Sysdev: 0.225; Positv: 1.000; Valcen: 0.820; Smooth: 0.992

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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	CHEY PROTEIN
Molecular weight formula_weight	13234.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1840

MGKRVLIVDDAAFMRMMLKDIITKAGYEVAGEATNGREAVEKYKELKPDIVTMDITMPEMNGIDAIKEIMKIDPNAKIIVCSAMGQQAMVIEAIKAGAKDFIVKPFQPSRVVEALNKVSK

来源 Source

来源生物 organism	Thermotoga maritima
NCBI Class编号 ncbi_taxonomy_id	2336
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	38

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3tmya_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.1 — CheY-like
Family Family family	c.23.1.1 — CheY-related

Domain ID domain_id	d3tmyb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.1 — CheY-like
Family Family family	c.23.1.1 — CheY-related

CATH v4.4 (2 domains)

Domain ID domain_id	3tmyA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

Domain ID domain_id	3tmyB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

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8. Citations (3)

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Unit-cell length a length_a	109.658 Å
Unit-cell length b length_b	64.719 Å
Unit-cell length c length_c	33.810 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1820
R_free r_free	—

fit	/app/data/saxs_computation/tm/3tmy/3tmy.fit
pddf	/app/data/pr_computation/tm/3tmy/3tmy.pr.out
profile	/app/data/saxs_computation/tm/3tmy/3tmy.dat

CHEY FROM THERMOTOGA MARITIMA (MN-III)

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

CHEY PROTEIN

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