SAXSdb — 5xtm

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

50S ribosomal protein L7Ae

Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)

UniProt P62009

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Monomer	Protein 1 RNA 1	RNA (47-MER) × 1 MAGNESIUM ION × 13 water × 2	Consistent with all polymers
2	Protein–RNA	Monomer	Protein 1 RNA 1	RNA (47-MER) × 1 MAGNESIUM ION × 11 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL7A_PYRHO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–124； UniProt 1–123 Author chain C； PDBConstruct 2–124； UniProt 1–123

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	5xtm
Deposition date deposition_date	2017-06-20
Structure title title	Crystal structure of PhoRpp38 bound to a K-turn in P12.2 helix
Keywords keywords	RNA-Protein Complex, Rnase P, Kink turn, RNA BINDING PROTEIN, RNA BINDING PROTEIN-RNA complex; RNA BINDING PROTEIN/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.

5xtm__assembly_1__model_1

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

Download this curve (.dat)

5xtm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5xtm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.66 Å
Rg (electron density)	22.84 Å
Total Rg	23.48 Å
Atom count	1967
Residues	167
Excluded volume	31488 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5xtm__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5xtm__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	50S ribosomal protein L7Ae
Molecular weight formula_weight	14645.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	4251

MMAKPSYVKFEVPKELAEKALQAVEIARDTGKIRKGTNETTKAVERGQAKLVIIAEDVDPEEIVAHLPPLCEEKEIPYIYVPSKKELGAAAGIEVAAASVAIIEPGKARDLVEEIAMKVRELMKLEHHHHHH

Source Source

Source organism organism	Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
NCBI taxonomy ID ncbi_taxonomy_id	70601
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	RNA (47-MER)
Molecular weight formula_weight	15466.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	B,D

GGUAUGGGAUGAAAGCGGUGAAGGGAAACCGAGUUAACCCCUAAGCC

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	24

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	306

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5xtmA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	30 — Ribosomal protein L30/S12

Domain ID domain_id	5xtmC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1330 — 60s Ribosomal Protein L30; Chain: A;
Homologous superfamily homologous superfamily	30 — Ribosomal protein L30/S12

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Unit-cell length a length_a	52.070 Å
Unit-cell length b length_b	71.720 Å
Unit-cell length c length_c	91.280 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.58 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	39.264 Å
R factor r_factor	0.1981
R_work r_work	0.1969
R_free r_free	0.2221

Crystal structure of PhoRpp38 bound to a K-turn in P12.2 helix

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

50S ribosomal protein L7Ae

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

5xtm__assembly_1__model_1

5xtm__assembly_1__model_1 | I(q)

5xtm__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of PhoRpp38 bound to a K-turn in P12.2 helix

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

50S ribosomal protein L7Ae

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

5xtm__assembly_1__model_1

5xtm__assembly_1__model_1 | I(q)

5xtm__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)