SAXSdb — 3af6

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

Putative uncharacterized protein PH1404

Pyrococcus horikoshii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Monomer	Protein 1 RNA 2	5'-R((SSU)P(SSU)P(SSU)P(SSU)P(SSU)P(SSU))-3' × 2 SULFATE ION × 5 ZINC ION × 2 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O50112_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–651； UniProt 1–651

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	3af6
Deposition date deposition_date	2010-02-24
Structure title title	The crystal structure of an archaeal CPSF subunit, PH1404 from Pyrococcus horikoshii complexed with RNA-analog
Keywords keywords	;archaeal CPSF, beta-CASP family, KH domain, ribonuclease, metallo-beta-lactamase superfamily, Pyrococcus horikoshii, archaea, RNA-analog, HYDROLASE-RNA complex ;; HYDROLASE/RNA
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.

3af6__assembly_1__model_1

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

Download this curve (.dat)

3af6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3af6__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.77 Å
Rg (electron density)	25.72 Å
Total Rg	26.63 Å
Atom count	5232
Residues	637
Excluded volume	93439 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3af6__assembly_1__model_1`	trimeric （3）	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	Putative uncharacterized protein PH1404
Molecular weight formula_weight	74055.6 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	5269

MTFLIKRETQVDQILRDIRAVVNQMVPKEAKITEIEFEGPELVIYVKNPEAIMKDGELIKDLAKVLKKRISVRPDPEVLLPPEEAEKLIFEIVPKEAEITNIAFDPSVGEVLIEAKKPGLVIGKNGETLRLITQKVKWAPKVVRTPPLQSQTIYSIRQILQTESKDRRKFLRQVGRNIYRKPEYKSRWIRITGLGGFREVGRSALLVQTDESFVLVDFGVNVAMLNDPYKAFPHFDAPEFQYVLREGLLDAIIITHAHLDHCGMLPYLFRYNLFDGPIYTTPPTRDLMVLLQKDFIEIQQSNGQDPLYRPRDIKEVIKHTITLDYGEVRDISPDIRLTLHNAGHILGSAIVHLHIGNGLHNIAITGDFKFIPTRLLEPANAKFPRLETLVMESTYGGANDIQMPREEAEKRLIEVIHNTIKRGGKVLIPAMAVGRAQEVMMVLEEYARIGGIEVPIYLDGMIWEATAIHTAYPEYLSRRLREQIFKEGYNPFLSEIFHPVANSRERQDIIDSNEPAIIIASSGMLVGGPSVEYFKQLAPDPKNSIIFVSYQAEGTLGRQVQSGIREIPMVGEEGRTEVIKVNMEVHTIDGFSGHADRRELMNYVAKVRPRPERIITVHGEPQKCLDLATSIHRKFGISTRAPNNLDTIRLR

Source Source

Source organism organism	Pyrococcus horikoshii
NCBI taxonomy ID ncbi_taxonomy_id	70601
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	5'-R((SSU)P(SSU)P(SSU)P(SSU)P(SSU)P(SSU))-3'
Molecular weight formula_weight	1888.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	B,C

UUUUUU

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 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	37

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3af6A01
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	3af6A02
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	3af6A03
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	3af6A04
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	86.438 Å
Unit-cell length b length_b	86.438 Å
Unit-cell length c length_c	237.501 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	42.590 Å
R factor r_factor	0.2200
R_work r_work	0.2200
R_free r_free	0.2580

The crystal structure of an archaeal CPSF subunit, PH1404 from Pyrococcus horikoshii complexed with RNA-analog

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

Putative uncharacterized protein PH1404

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

3af6__assembly_1__model_1

3af6__assembly_1__model_1 | I(q)

3af6__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

The crystal structure of an archaeal CPSF subunit, PH1404 from Pyrococcus horikoshii complexed with RNA-analog

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

Putative uncharacterized protein PH1404

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

3af6__assembly_1__model_1

3af6__assembly_1__model_1 | I(q)

3af6__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)