SAXSdb — 1wn9

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

the hypothetical protein (TT1805)

Thermus thermophilus

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 1–131	Non-standard monomer：Yes (specific site not provided by mmCIF)	ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；14% PEG 8000, 0.1M NaCacodylate, 170mM ZnAcetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.58 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 1WN9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1WNA Crystal structure of the hypothetical protein TT1805 from Thermus thermophillus HB8 Deposited 2004-07-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–131（131 aa）	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；293 K；13% PEG 8000, 20% glycerol, 40mM Potassium dihydrogen phosphate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.58 Å R-free 0.229
4HEA Crystal structure of the entire respiratory complex I from Thermus thermophilus Deposited 2012-10-03	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain W 1–131（131 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 7 FMN FLAVIN MONONUCLEOTIDE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；100 mM Bis-Tris pH 6.0, 19% (w/v) polyethylene glycol (PEG) 4000, 100 mM KCl, 100 mM glutaric acid pH 6.0 and 2.2 mM FOS-CHOLINE-8 fluorinated , VAPOR DIFFUSION, SITTING DROP, temperature 295K X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；100 mM Bis-Tris pH 6.0, 24% (w/v) polyethylene glycol (PEG) 4000, 100 mM KCl, 100 mM glutaric acid pH 6.0 and 50 mM NDSB-201, VAPOR DIFFUSION, SITTING DROP, temperature 295K X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；100 mM Bis-Tris pH 6.0, 26% (w/v) polyethylene glycol (PEG) 4000, 100 mM KCl, 100 mM glutaric acid pH 6.0 and 0.6% DDM, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.30 Å R-free 0.239
4HEA Crystal structure of the entire respiratory complex I from Thermus thermophilus Deposited 2012-10-03	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain X 1–131（131 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 7 FMN FLAVIN MONONUCLEOTIDE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；100 mM Bis-Tris pH 6.0, 19% (w/v) polyethylene glycol (PEG) 4000, 100 mM KCl, 100 mM glutaric acid pH 6.0 and 2.2 mM FOS-CHOLINE-8 fluorinated , VAPOR DIFFUSION, SITTING DROP, temperature 295K X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；100 mM Bis-Tris pH 6.0, 24% (w/v) polyethylene glycol (PEG) 4000, 100 mM KCl, 100 mM glutaric acid pH 6.0 and 50 mM NDSB-201, VAPOR DIFFUSION, SITTING DROP, temperature 295K X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；100 mM Bis-Tris pH 6.0, 26% (w/v) polyethylene glycol (PEG) 4000, 100 mM KCl, 100 mM glutaric acid pH 6.0 and 0.6% DDM, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.30 Å R-free 0.239
6I0D Respiratory complex I from Thermus thermophilus with bound Decyl-Ubiquinone Deposited 2018-10-25	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain W 1–131（131 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 7 FMN FLAVIN MONONUCLEOTIDE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2 DCQ 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；296 K；100 mM Bis-Tris pH 6.0, 23% (w/v) polyethylene glycol (PEG) 4000, 100 mM KCl, 100 mM glutaric acid pH 6.0 and 50 mM NDSB-201	Resolution 3.60 Å R-free 0.225
6I0D Respiratory complex I from Thermus thermophilus with bound Decyl-Ubiquinone Deposited 2018-10-25	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain X 1–131（131 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 7 FMN FLAVIN MONONUCLEOTIDE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2 DCQ 2-decyl-5,6-dimethoxy-3-methylcyclohexa-2,5-diene-1,4-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；296 K；100 mM Bis-Tris pH 6.0, 23% (w/v) polyethylene glycol (PEG) 4000, 100 mM KCl, 100 mM glutaric acid pH 6.0 and 50 mM NDSB-201	Resolution 3.60 Å R-free 0.225
6I1P Respiratory complex I from Thermus thermophilus with bound NADH Deposited 2018-10-29	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain W 1–131（131 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 7 FMN FLAVIN MONONUCLEOTIDE × 1 NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；296 K；100 mM Bis-Tris pH 6.0, 23% (w/v) PEG 4000, 100 mM KCl, 100 mM glutaric acid pH 6.0 and 0.01 mM n-tetradecyl-beta-D-maltopyranoside	Resolution 3.21 Å R-free 0.231
6I1P Respiratory complex I from Thermus thermophilus with bound NADH Deposited 2018-10-29	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain X 1–131（131 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 7 FMN FLAVIN MONONUCLEOTIDE × 1 NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；296 K；100 mM Bis-Tris pH 6.0, 23% (w/v) PEG 4000, 100 mM KCl, 100 mM glutaric acid pH 6.0 and 0.01 mM n-tetradecyl-beta-D-maltopyranoside	Resolution 3.21 Å R-free 0.231
6Q8O Respiratory complex I from Thermus thermophilus with bound Piericidin A Deposited 2018-12-15	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain W 1–131（131 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 7 FMN FLAVIN MONONUCLEOTIDE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2 HQH Piericidin A × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；296 K；100 mM Bis-Tris pH 6.0, 24% (w/v) PEG 4000, 100 mM KCl, 100 mM glutaric acid and 0.59 mM n-undecyl-beta-maltoside	Resolution 3.60 Å R-free 0.235
6Q8O Respiratory complex I from Thermus thermophilus with bound Piericidin A Deposited 2018-12-15	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain X 1–131（131 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 7 FMN FLAVIN MONONUCLEOTIDE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2 HQH Piericidin A × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；296 K；100 mM Bis-Tris pH 6.0, 24% (w/v) PEG 4000, 100 mM KCl, 100 mM glutaric acid and 0.59 mM n-undecyl-beta-maltoside	Resolution 3.60 Å R-free 0.235
6Q8W Respiratory complex I from Thermus thermophilus with bound Aureothin. Deposited 2018-12-16	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain W 1–131（131 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 7 FMN FLAVIN MONONUCLEOTIDE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2 HQW Aureothin × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；296 K；100 mM Bis-Tris pH 6.0, 25% (w/v) PEG 4000, 100 mM KCl, 100 mM glutaric acid and 7.6 mM 4-cyclohexyl-1-butyl-beta-D-maltoside	Resolution 3.40 Å R-free 0.234
6Q8W Respiratory complex I from Thermus thermophilus with bound Aureothin. Deposited 2018-12-16	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain X 1–131（131 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 7 FMN FLAVIN MONONUCLEOTIDE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2 HQW Aureothin × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；296 K；100 mM Bis-Tris pH 6.0, 25% (w/v) PEG 4000, 100 mM KCl, 100 mM glutaric acid and 7.6 mM 4-cyclohexyl-1-butyl-beta-D-maltoside	Resolution 3.40 Å R-free 0.234
6Q8X Respiratory complex I from Thermus thermophilus with bound Pyridaben. Deposited 2018-12-16	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain W 1–131（131 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 7 FMN FLAVIN MONONUCLEOTIDE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2 HQK Pyridaben × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；296 K；100 mM Bis-Tris pH 6.0, 21% (w/v) PEG 4000, 100 mM KCl, 100 mM glutaric acid and 1.02 mM octyl-maltoside fluorinated	Resolution 3.51 Å R-free 0.232
6Q8X Respiratory complex I from Thermus thermophilus with bound Pyridaben. Deposited 2018-12-16	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain X 1–131（131 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 7 FMN FLAVIN MONONUCLEOTIDE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2 HQK Pyridaben × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；296 K；100 mM Bis-Tris pH 6.0, 21% (w/v) PEG 4000, 100 mM KCl, 100 mM glutaric acid and 1.02 mM octyl-maltoside fluorinated	Resolution 3.51 Å R-free 0.232
6Y11 Respiratory complex I from Thermus thermophilus Deposited 2020-02-10	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain W 1–131（131 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 7 FMN FLAVIN MONONUCLEOTIDE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；100 mM Bis-Tris pH 6.0, 26% (w/v) polyethylene glycol (PEG) 4000, 100 mM KCl, 100 mM glutaric acid pH 6.0 and 0.6% DDM	Resolution 3.11 Å R-free 0.229
6Y11 Respiratory complex I from Thermus thermophilus Deposited 2020-02-10	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain X 1–131（131 aa）	Not recorded	SF4 IRON/SULFUR CLUSTER × 7 FMN FLAVIN MONONUCLEOTIDE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；100 mM Bis-Tris pH 6.0, 26% (w/v) polyethylene glycol (PEG) 4000, 100 mM KCl, 100 mM glutaric acid pH 6.0 and 0.6% DDM	Resolution 3.11 Å R-free 0.229

8 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q5SI52_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–131； UniProt 1–131

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	1wn9
Deposition date deposition_date	2004-07-28
Structure title title	Crystal structure of the hypothetical protein TT1805 from Thermus thermophillus HB8
Keywords keywords	Thermus thermophillus, STRUCTURAL GENOMICS, RIKEN Structural Genomics/Proteomics Initiative, RSGI, UNKNOWN FUNCTION; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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	14.89 Å
Radius of gyration Rg (electron density) rg_electron	13.36 Å
Forward intensity I(0) i0	3772650.00
Molecular weight molecular_weight	14050.0 kDa
Excluded volume excluded_volume	17734 Å³
Envelope volume envelope_volume	19515 Å³
Hydration-shell volume shell_volume	12232 Å³
Envelope diameter envelope_diameter	45.3 Å
Shell Rg shell_rg	19.39 Å
Envelope Rg envelope_rg	13.69 Å
Shape Rg shape_rg	13.34 Å
Total Rg total_rg	14.72 Å
Total atoms total_atoms	975
Residues n_residues	123
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	46.9 Å
Rg (real space) rg_real	14.76 Å
Rg uncertainty (real space) rg_real_error	0.20 Å
I(0) (real space) i0_real	3.7730e+06
I(0) uncertainty (real space) i0_real_error	3.5940e+04
Rg (reciprocal space) rg_reciprocal	14.77 Å
I(0) (reciprocal space) i0_reciprocal	3773000.0000
Solution quality estimate total_estimate	0.8059
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.8 Å
Skewness Skewness skewness	0.030
Kurtosis Kurtosis kurtosis	-0.397
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	899500.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.829; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; 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	the hypothetical protein (TT1805)
Molecular weight formula_weight	14389.2 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	1079

MVRVGMRAAPRVSLEALKAALGGLKLSEAKVYLITDWQDKRDQARYALLLHTGKKDLLVPDAFGPAFPGGEEALSELVGLLLAQGARRFYEAVVSPGEMTALLDLPPEELLKRVMAIANPTDPGIYLKRAA

来源 Source

来源生物 organism	Thermus thermophilus
NCBI Class编号 ncbi_taxonomy_id	300852
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 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	104

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1wn9a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.319 — TTHA1528-like
Superfamily Superfamily superfamily	d.319.1 — TTHA1528-like
Family Family family	d.319.1.1 — TTHA1528-like

CATH v4.4 (1 domains)

Domain ID domain_id	1wn9A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1530 — hypothetical protein tt1805
Homologous superfamily homologous superfamily	10 — TTHA1528-like

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8. Citations (1)

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Unit-cell length a length_a	74.661 Å
Unit-cell length b length_b	53.997 Å
Unit-cell length c length_c	36.201 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.93 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.580 Å
Low-resolution limit resolution_low	34.120 Å
R factor r_factor	0.2140
R_work r_work	0.2140
R_free r_free	0.2460

fit	/app/data/saxs_computation/wn/1wn9/1wn9.fit
pddf	/app/data/pr_computation/wn/1wn9/1wn9.pr.out
profile	/app/data/saxs_computation/wn/1wn9/1wn9.dat

Crystal structure of the hypothetical protein TT1805 from Thermus thermophillus HB8

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

the hypothetical protein (TT1805)

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