SAXSdb — 2ycb

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

CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR

METHANOTHERMOBACTER THERMAUTOTROPHICUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 5 PHOSPHATE ION × 4 POTASSIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O27271_METTH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–636； UniProt 1–636 Author chain B； PDBConstruct 1–636； UniProt 1–636

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	2ycb
Deposition date deposition_date	2011-03-13
Structure title title	Structure of the archaeal beta-CASP protein with N-terminal KH domains from Methanothermobacter thermautotrophicus
Keywords keywords	HYDROLASE, BETA-CASP, RNASE, KH, METALLO-BETA-LACTAMASE; HYDROLASE
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.

2ycb__assembly_1__model_1

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

Download this curve (.dat)

2ycb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ycb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.78 Å
Rg (electron density)	38.56 Å
Total Rg	38.90 Å
Atom count	10256
Residues	1269
Excluded volume	182830 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ycb__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 (5)

Entity 1 Entity 1 polymer

Description description	CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR
Molecular weight formula_weight	72990.7 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	10285

MVSEMLEEIKRTIMQRLPERVQVAKVEFEGPEVVIYTKNPEIITENGNLIRDIAKDIRKRIIIRSDRSVLMDPEKAIRKIHEIVPEEAKITNISFDDVTCEVIIEARKPGLVIGKYGSTSREIVKNTGWAPKILRTPPISSEIIERIRRTLRKNSKERKKILQQLGNRIHQKPKYDNDWARLTAMGGFREVGRSCLYLQTPNSRVLLDCGVNVAGGDDKNSYPYLNVPEFTLDSLDAVIITHAHLDHSGFLPYLYHYGYDGPVYCTAPTRDLMTLLQLDHIDIAHREDEPLPFNVKHVKKSVKHTITLDYGEVTDIAPDIRLTLHNAGHILGSAMAHLHIGDGQHNMVYTGDFKYEQSRLLEAAANRFPRIETLVMESTYGGHEDVQPSRNRAEKELVKTIYSTLRRGGKILIPVFAVGRAQELMIVLEEYIRTGIIDEVPVYIDGMIWEANAIHTARPEYLSKDLRDQIFHMGHNPFISDIFHKVNGMDERREIVEGEPSIILSTSGMLTGGNSLEYFKWLCEDPDNSLVFVGYQAEGSLGRRIQKGWKEIPLKDEDDKMRVYNVRMNIKTIEGFSGHSDRRQLMEYVKRISPKPEKILLCHGDNYKTLDLASSIYRTYRIETKTPLNLETVRIQ

Source Source

Source organism organism	METHANOTHERMOBACTER THERMAUTOTROPHICUS
NCBI taxonomy ID ncbi_taxonomy_id	187420
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	29

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	2ycbA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	2ycbA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	20 — K homology (KH) domain

Domain ID domain_id	2ycbA03
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	15 — Metallo-beta-lactamase; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

Domain ID domain_id	2ycbA04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10890 —

Domain ID domain_id	2ycbB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	2ycbB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	20 — K homology (KH) domain

Domain ID domain_id	2ycbB03
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	15 — Metallo-beta-lactamase; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

Domain ID domain_id	2ycbB04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10890 —

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Unit-cell length a length_a	112.027 Å
Unit-cell length b length_b	112.027 Å
Unit-cell length c length_c	400.608 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	16

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2154
R_work r_work	0.2146
R_free r_free	0.2508

Structure of the archaeal beta-CASP protein with N-terminal KH domains from Methanothermobacter thermautotrophicus

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

CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR

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

2ycb__assembly_1__model_1

2ycb__assembly_1__model_1 | I(q)

2ycb__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

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Structure of the archaeal beta-CASP protein with N-terminal KH domains from Methanothermobacter thermautotrophicus

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

CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR

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

2ycb__assembly_1__model_1

2ycb__assembly_1__model_1 | I(q)

2ycb__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

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)