SAXSdb — 1xml

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

No usable UniProt protein identity is available for this entry.

The relationship tables retain this entry's assembly and composition data, but cross-PDB links for the same protein cannot be established reliably without a unified protein identity.

Assembly Composition of the Current Entry

Assembly	Physical composition	Protein state	蛋白 / DNA / RNA / 其他Polymer	Data consistency
1	Protein homooligomer	Homooligomer	2 / 0 / 0 / 0	Consistent with protein count

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	1xml
Deposition date deposition_date	2004-10-04
Structure title title	Structure of human Dcps
Keywords keywords	scavenger Decapping Enzyme, CHAPERONE; CHAPERONE
Experimental Method method	X-RAY DIFFRACTION

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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.

1xml__assembly_1__model_1

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

Download this curve (.dat)

1xml__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1xml__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.49 Å
Rg (electron density)	26.26 Å
Total Rg	27.12 Å
Atom count	4723
Residues	566
Excluded volume	84058 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1xml__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	heat shock-like protein 1
Molecular weight formula_weight	39110.3 kDa
Mutation mutation	L206M, L317M
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	5177

GPLGSMADAAPQLGKRKRELDVEEAHAASTEEKEAGVGNGTCAPVRLPFSGFRLQKVLRESARDKIIFLHGKVNEASGDGDGEDAVVILEKTPFQVEQVAQLLTGSPELQLQFSNDIYSTYHLFPPRQLNDVKTTVVYPATEKHLQKYLRQDLRLIRETGDDYRNITLPHLESQSLSIQWVYNILDKKAEADRIVFENPDPSDGFVLIPDMKWNQQQLDDLYLIAICHRRGIRSLRDLTPEHLPLLRNILHQGQEAILQRYRMKGDHLRVYLHYLPSYYHLHVHFTALGFEAPGSGVERAHLLAEVIENLECDPRHYQQRTMTFALRADDPLLKLLQEAQQS

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 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	454

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1xmla1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.13 — HIT-like
Superfamily Superfamily superfamily	d.13.1 — HIT-like
Family Family family	d.13.1.3 — mRNA decapping enzyme DcpS C-terminal domain

Domain ID domain_id	d1xmla2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.246 — mRNA decapping enzyme DcpS N-terminal domain
Superfamily Superfamily superfamily	d.246.1 — mRNA decapping enzyme DcpS N-terminal domain
Family Family family	d.246.1.0 — automated matches

Domain ID domain_id	d1xmlb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.13 — HIT-like
Superfamily Superfamily superfamily	d.13.1 — HIT-like
Family Family family	d.13.1.3 — mRNA decapping enzyme DcpS C-terminal domain

Domain ID domain_id	d1xmlb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.246 — mRNA decapping enzyme DcpS N-terminal domain
Superfamily Superfamily superfamily	d.246.1 — mRNA decapping enzyme DcpS N-terminal domain
Family Family family	d.246.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	1xmlA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	40 — Scavenger mRNA decapping enzyme, N-terminal domain

Domain ID domain_id	1xmlA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	428 — HIT family, subunit A
Homologous superfamily homologous superfamily	10 — HIT-like

Domain ID domain_id	1xmlB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	40 — Scavenger mRNA decapping enzyme, N-terminal domain

Domain ID domain_id	1xmlB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	428 — HIT family, subunit A
Homologous superfamily homologous superfamily	10 — HIT-like

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Unit-cell length a length_a	101.922 Å
Unit-cell length b length_b	103.863 Å
Unit-cell length c length_c	71.067 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2211
R_work r_work	0.2195
R_free r_free	0.2526

Structure of human Dcps