SAXSdb — 6h57

▼

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

Probable ATP-dependent RNA helicase DHR1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	1,2-ETHANEDIOL × 14 MAGNESIUM ION × 1 CHLORIDE ION × 4 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DHR1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1267； UniProt 1–1267

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6h57
Deposition date deposition_date	2018-07-24
Structure title title	Crystal structure of S. cerevisiae DEAH-box RNA helicase Dhr1, essential for small ribosomal subunit biogenesis
Keywords keywords	protein, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6h57__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6h57__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6h57__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	32.09 Å
Rg (electron density)	31.29 Å
Total Rg	31.78 Å
Atom count	6401
Residues	795
Excluded volume	115330 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6h57__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Probable ATP-dependent RNA helicase DHR1
Molecular weight formula_weight	145171.4 kDa
EC 编号 ec_number	3.6.4.13
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	6697

MGTYRKRFNEKARSGHMAKLKELKRIRNKQFTRQDENDERVENPDSAPAESSTTEPNANAEILEPLTEEEKKMKKRKLQELFTPKESKVSRLKKKRLDKFIEHQLKREERKTIIGKLQDYKIDTSLLTSSKRLGEGRQTKKEEFKEALSLERQGRGNEQTNEILYEEYEPKVWDEYGEGGSSEDDDGEDDFEASFGSMPKPTDNEEKKSSGFIDHRPAKFGGSGLSFGFSNIKVINKESKTPKKKYNWRQRVEMEELKKHGKEDEMDFDTTSEDDDEEEDQEEEDKMHPSENPLEEVESADSETGSEKFDQNDVANEFKDWANQEIKKLEGRDQELVTPTLNIDYKPIIRKEDLDDGLQEAYVPINENSTRKAFYVEVSRSDEIQKARIQLPVFGEEHKIMEAIHHNDVVIICGETGSGKTTQVPQFLYEAGFGAEDSPDYPGMVGITQPRRVAAVSMAERVANELGDHGHKVGYQIRFDSTAKEDTKVKFMTDGVLLREMMHDFKLTKYSSIIIDEAHERNINTDILIGMLSRCVRLRAKLHKENPIEHKKLKLIIMSATLRVSDFSENKTLFPIAPPVLQVDARQFPVSIHFNRRTAFNYTDEAFRKTCKIHQKLPPGAILVFLTGQQEITHMVKRLRKEFPFKKNSKYNKDLETPVSKMGINSKTTDLEAEDIDFSVQVIDQDKFKSAIRYEEDEGNSGNGEDEEDEEEEGFEEVLTEGQTANDPLYVLPLYSLLPTKEQMRVFQKPPQGSRLCIVATNVAETSLTIPGVRYVVDSGRSKERKYNESNGVQSFEVGWVSKASANQRSGRAGRTGPGHCYRLYSSAVFEHDFEQFSKPEILRMPVESIVLQMKSMAIHNIINFPFPTPPDRVALSKAIQLLQYLGALDNKEMITEDGKKMSLFPLSPRFSKMLLVSDEKACLPYIVAIVSALSVGDPFINEFELGINEISRKPNPDENLDDKIREHDESTPGMDPELKKELRSKFYKSRSQFSKLDKFSDVFRLLSVVSAMDYVPKEQKEIFMKKNFLRGKLMEEIVKLRKQLMYIIKSNTSKENIAVVIRNEDLKSDIPSVIQIKLLKQMICAGFVDHVAVRADVLFPDDAKITNRTSIINIPYIPVLATRTPNIEDCFVYIHPTSILNNLGEMPPKYMLYYSLHLGGNNKTRMNTLCDIASTPLANIARKGLLLTYSKPLTGQGLKTVNLSPTERYCYVVPRFGSTVDNDLKIGWDLNPIAVHQKKQKGQWTVIKFITRKGFQTITGEEKEKK

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	274

▶

Unit-cell length a length_a	57.314 Å
Unit-cell length b length_b	115.800 Å
Unit-cell length c length_c	157.479 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	48.830 Å
R factor r_factor	0.2070
R_work r_work	0.2050
R_free r_free	0.2450

Crystal structure of S. cerevisiae DEAH-box RNA helicase Dhr1, essential for small ribosomal subunit biogenesis

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

Probable ATP-dependent RNA helicase DHR1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6h57__assembly_1__model_1

6h57__assembly_1__model_1 | I(q)

6h57__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Crystal structure of S. cerevisiae DEAH-box RNA helicase Dhr1, essential for small ribosomal subunit biogenesis

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

Probable ATP-dependent RNA helicase DHR1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6h57__assembly_1__model_1

6h57__assembly_1__model_1 | I(q)

6h57__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)