SAXSdb — 1k9v

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

Amidotransferase hisH

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 F； UniProt 1–201	Not recorded	ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；PEG 200, sodium acetate, DTT, calcium chloride, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.40 Å R-free 0.278

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 1K9V	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GPW Structural evidence for ammonia tunneling across the (beta/alpha)8 barrel of the imidazole glycerol phosphate synthase bienzyme complex. Deposited 2001-11-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–201（201 aa）	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；PROTEIN SOLUTION: 10 MM TRIS (PH 8.0), 1 MM DTT, 1 MM EDTA, 28.8 MG/ML PROTEIN COMPLEX. PRECIPITATE SOLUTION: 15 %[W/V] PEG-8000, 0.9 M AMMONIUM NITRATE, 0.1 M HEPES/HCL (PH 8.5), 10 MM DTT, 5% [V/V] MPD	Resolution 2.40 Å R-free 0.290
1GPW Structural evidence for ammonia tunneling across the (beta/alpha)8 barrel of the imidazole glycerol phosphate synthase bienzyme complex. Deposited 2001-11-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–201（201 aa）	Not recorded	PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；PROTEIN SOLUTION: 10 MM TRIS (PH 8.0), 1 MM DTT, 1 MM EDTA, 28.8 MG/ML PROTEIN COMPLEX. PRECIPITATE SOLUTION: 15 %[W/V] PEG-8000, 0.9 M AMMONIUM NITRATE, 0.1 M HEPES/HCL (PH 8.5), 10 MM DTT, 5% [V/V] MPD	Resolution 2.40 Å R-free 0.290
1GPW Structural evidence for ammonia tunneling across the (beta/alpha)8 barrel of the imidazole glycerol phosphate synthase bienzyme complex. Deposited 2001-11-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–201（201 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；PROTEIN SOLUTION: 10 MM TRIS (PH 8.0), 1 MM DTT, 1 MM EDTA, 28.8 MG/ML PROTEIN COMPLEX. PRECIPITATE SOLUTION: 15 %[W/V] PEG-8000, 0.9 M AMMONIUM NITRATE, 0.1 M HEPES/HCL (PH 8.5), 10 MM DTT, 5% [V/V] MPD	Resolution 2.40 Å R-free 0.290
1KXJ The Crystal Structure of Glutamine Amidotransferase from Thermotoga maritima Deposited 2002-01-31	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–201（201 aa）	Not recorded	PO4 PHOSPHATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；2 M mono-Ammonium dihydrogen Phosphate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K	Resolution 2.80 Å R-free 0.274
1KXJ The Crystal Structure of Glutamine Amidotransferase from Thermotoga maritima Deposited 2002-01-31	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–201（201 aa）	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；2 M mono-Ammonium dihydrogen Phosphate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K	Resolution 2.80 Å R-free 0.274
2WJZ Crystal structure of (HisH) K181A Y138A mutant of imidazoleglycerolphosphate synthase (HisH HisF) which displays constitutive glutaminase activity Deposited 2009-06-02	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 B 1–201（201 aa）	Mutation：YES	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；PEG8K 10-12%, 100 MM HEPES PH = 8.5 22.5MM NH4NO3 / NH4AC 5% (V/V) MPD 10 MM DTT 20 MM L-GLN PROT. CONC.= 12 MG/ML	Resolution 2.60 Å R-free 0.218
2WJZ Crystal structure of (HisH) K181A Y138A mutant of imidazoleglycerolphosphate synthase (HisH HisF) which displays constitutive glutaminase activity Deposited 2009-06-02	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–201（201 aa）	Mutation：YES	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；PEG8K 10-12%, 100 MM HEPES PH = 8.5 22.5MM NH4NO3 / NH4AC 5% (V/V) MPD 10 MM DTT 20 MM L-GLN PROT. CONC.= 12 MG/ML	Resolution 2.60 Å R-free 0.218
2WJZ Crystal structure of (HisH) K181A Y138A mutant of imidazoleglycerolphosphate synthase (HisH HisF) which displays constitutive glutaminase activity Deposited 2009-06-02	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–201（201 aa）	Mutation：YES	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；PEG8K 10-12%, 100 MM HEPES PH = 8.5 22.5MM NH4NO3 / NH4AC 5% (V/V) MPD 10 MM DTT 20 MM L-GLN PROT. CONC.= 12 MG/ML	Resolution 2.60 Å R-free 0.218
3ZR4 STRUCTURAL EVIDENCE FOR AMMONIA TUNNELING ACROSS THE (BETA-ALPHA)8 BARREL OF THE IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE BIENZYME COMPLEX Deposited 2011-06-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–201（201 aa）	Not recorded	GOL GLYCEROL × 3 GLN GLUTAMINE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.41 Å R-free 0.258
3ZR4 STRUCTURAL EVIDENCE FOR AMMONIA TUNNELING ACROSS THE (BETA-ALPHA)8 BARREL OF THE IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE BIENZYME COMPLEX Deposited 2011-06-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–201（201 aa）	Not recorded	GOL GLYCEROL × 2 GLN GLUTAMINE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.41 Å R-free 0.258
3ZR4 STRUCTURAL EVIDENCE FOR AMMONIA TUNNELING ACROSS THE (BETA-ALPHA)8 BARREL OF THE IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE BIENZYME COMPLEX Deposited 2011-06-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–201（201 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.41 Å R-free 0.258
6RTZ Light-Regulation of Imidazole Glycerol Phosphate Synthase by Interference with its Allosteric Machinery through Photo-Sensitive Unnatural Amino Acids Deposited 2019-05-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–201（201 aa）	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG	Resolution 2.87 Å R-free 0.336
6RU0 Light-Regulation of Imidazole Glycerol Phosphate Synthase by Interference with its Allosteric Machinery through Photo-Sensitive Unnatural Amino Acids Deposited 2019-05-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–201（201 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG	Resolution 2.65 Å R-free 0.272
6RU0 Light-Regulation of Imidazole Glycerol Phosphate Synthase by Interference with its Allosteric Machinery through Photo-Sensitive Unnatural Amino Acids Deposited 2019-05-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–201（201 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG	Resolution 2.65 Å R-free 0.272
6RU0 Light-Regulation of Imidazole Glycerol Phosphate Synthase by Interference with its Allosteric Machinery through Photo-Sensitive Unnatural Amino Acids Deposited 2019-05-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–201（201 aa）	Not recorded	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；PEG	Resolution 2.65 Å R-free 0.272
6YMU Imidazole Glycerol Phosphate Synthase Deposited 2020-04-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–201（201 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, SITTING DROP；295 K；PEG	Resolution 2.11 Å R-free 0.250
6YMU Imidazole Glycerol Phosphate Synthase Deposited 2020-04-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–201（201 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, SITTING DROP；295 K；PEG	Resolution 2.11 Å R-free 0.250
6YMU Imidazole Glycerol Phosphate Synthase Deposited 2020-04-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 1–201（201 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, SITTING DROP；295 K；PEG	Resolution 2.11 Å R-free 0.250
7AC8 Molecular basis for the unique allosteric activation mechanism of the heterodimeric imidazole glycerol phosphate synthase complex. Deposited 2020-09-10	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 B 1–201（201 aa）	Mutation：C84A	GUO [(2R,3S,4R,5R)-5-[4-aminocarbonyl-5-[(E)-[[(2R,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]amino]methylideneamino]imidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate × 1 GLN GLUTAMINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；Pentaerythritol (5/4 PO/OH), sodium thiocyanate, HEPES, L-glutamine, ProFAR	Resolution 2.06 Å R-free 0.186
7AC8 Molecular basis for the unique allosteric activation mechanism of the heterodimeric imidazole glycerol phosphate synthase complex. Deposited 2020-09-10	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–201（201 aa）	Mutation：C84A	GLN GLUTAMINE × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；Pentaerythritol (5/4 PO/OH), sodium thiocyanate, HEPES, L-glutamine, ProFAR	Resolution 2.06 Å R-free 0.186
7AC8 Molecular basis for the unique allosteric activation mechanism of the heterodimeric imidazole glycerol phosphate synthase complex. Deposited 2020-09-10	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 1–201（201 aa）	Mutation：C84A	GUO [(2R,3S,4R,5R)-5-[4-aminocarbonyl-5-[(E)-[[(2R,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]amino]methylideneamino]imidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate × 1 GLN GLUTAMINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；Pentaerythritol (5/4 PO/OH), sodium thiocyanate, HEPES, L-glutamine, ProFAR	Resolution 2.06 Å R-free 0.186

8 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HIS5_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain F； PDBConstruct 1–201； UniProt 1–201

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	1k9v
Deposition date deposition_date	2001-10-31
Structure title title	Structural evidence for ammonia tunelling across the (beta-alpha)8-barrel of the imidazole glycerol phosphate synthase bienzyme complex
Keywords keywords	glutaminase, imidazole glycerol phosphate synthase, (beta-alpha)8-barrel, ammonia tunnel, TRANSFERASE; TRANSFERASE
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	17.27 Å
Radius of gyration Rg (electron density) rg_electron	15.77 Å
Forward intensity I(0) i0	8927150.00
Molecular weight molecular_weight	22381.0 kDa
Excluded volume excluded_volume	28170 Å³
Envelope volume envelope_volume	30943 Å³
Hydration-shell volume shell_volume	16184 Å³
Envelope diameter envelope_diameter	57.7 Å
Shell Rg shell_rg	22.16 Å
Envelope Rg envelope_rg	16.08 Å
Shape Rg shape_rg	15.75 Å
Total Rg total_rg	16.89 Å
Total atoms total_atoms	1578
Residues n_residues	200
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	56.0 Å
Rg (real space) rg_real	17.15 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	8.9270e+06
I(0) uncertainty (real space) i0_real_error	1.0600e+05
Rg (reciprocal space) rg_reciprocal	17.16 Å
I(0) (reciprocal space) i0_reciprocal	8927000.0000
Solution quality estimate total_estimate	0.7973
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	22.8 Å
Skewness Skewness skewness	0.129
Kurtosis Kurtosis kurtosis	-0.322
Angular range angular_range	— – 0.4600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2963000.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.790; Stabil: 0.999; 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	Amidotransferase hisH
Molecular weight formula_weight	23130.6 kDa
EC 编号 ec_number	2.4.2.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F
Atom count atom_count	1643

MRIGIISVGPGNIMNLYRGVKRASENFEDVSIELVESPRNDLYDLLFIPGVGHFGEGMRRLRENDLIDFVRKHVEDERYVVGVCLGMQLLFEESEEAPGVKGLSLIEGNVVKLRSRRLPHMGWNEVIFKDTFPNGYYYFVHTYRAVCEEEHVLGTTEYDGEIFPSAVRKGRILGFQFHPEKSSKIGRKLLEKVIECSLSRR

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	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	65

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1k9vf_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.16 — Class I glutamine amidotransferase-like
Family Family family	c.23.16.1 — Class I glutamine amidotransferases (GAT)

CATH v4.4 (1 domains)

Domain ID domain_id	1k9vF00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	880 — Class I glutamine amidotransferase (GATase) domain

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8. Citations (1)

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Unit-cell length a length_a	126.008 Å
Unit-cell length b length_b	35.837 Å
Unit-cell length c length_c	42.507 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	2.400 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2240
R_work r_work	0.2240
R_free r_free	0.2780

fit	/app/data/saxs_computation/k9/1k9v/1k9v.fit
pddf	/app/data/pr_computation/k9/1k9v/1k9v.pr.out
profile	/app/data/saxs_computation/k9/1k9v/1k9v.dat

Structural evidence for ammonia tunelling across the (beta-alpha)8-barrel of the imidazole glycerol phosphate synthase bienzyme complex

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

Amidotransferase hisH

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