SAXSdb — 9v5s

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

Elongation factor Tu

Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	GUANOSINE-5'-DIPHOSPHATE × 2 MAGNESIUM ION × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	GUANOSINE-5'-DIPHOSPHATE × 2 MAGNESIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EFTU_MYCPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–394； UniProt 1–394 Author chain B； PDBConstruct 1–394； UniProt 1–394 Author chain C； PDBConstruct 1–394； UniProt 1–394 Author chain D； PDBConstruct 1–394； UniProt 1–394

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	9v5s
Deposition date deposition_date	2025-05-26
Last revision last_revision	2025-10-29
Structure title title	Crystal structure of EF-Tu from Mycoplasma pneumoniae
Keywords keywords	Mycoplasma pneumoniae, EF-Tu, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
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.

9v5s__assembly_1__model_1

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

Download this curve (.dat)

9v5s__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9v5s__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.89 Å
Rg (electron density)	31.54 Å
Total Rg	32.10 Å
Atom count	5931
Residues	767
Excluded volume	105390 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9v5s__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9v5s__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	Elongation factor Tu
Molecular weight formula_weight	43212.3 kDa
EC 编号 ec_number	3.6.5.3
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	12463

MAREKFDRSKPHVNVGTIGHIDHGKTTLTAAICTVLAKEGKSAATRYDQIDKAPEEKARGITINSAHVEYSSDKRHYAHVDCPGHADYIKNMITGAAQMDGAILVVSATDSVMPQTREHILLARQVGVPRMVVFLNKCDIATDEEVQELVAEEVRDLLTSYGFDGKNTPIIYGSALKALEGDPKWEAKIHDLMNAVDEWIPTPEREVDKPFLLAIEDTMTITGRGTVVTGRVERGELKVGQEIEIVGLRPIRKAVVTGIEMFKKELDSAMAGDNAGVLLRGVDRKEVERGQVLAKPGSIKPHKKFKAEIYALKKEEGGRHTGFLNGYRPQFYFRTTDVTGSISLPENTEMVLPGDNTSITVELIAPIACEKGSKFSIREGGRTVGAGSVTEVLE

Source Source

Source organism organism	Mycoplasma pneumoniae (strain ATCC 29342 / M129 / Subtype 1)
Common name common_name	Mycoplasmoides pneumoniae
NCBI taxonomy ID ncbi_taxonomy_id	272634
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	4

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	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	647

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Unit-cell length a length_a	64.382 Å
Unit-cell length b length_b	106.733 Å
Unit-cell length c length_c	257.591 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.240 Å
Low-resolution limit resolution_low	23.200 Å
R factor r_factor	0.2045
R_work r_work	0.2036
R_free r_free	0.2421

Crystal structure of EF-Tu from Mycoplasma pneumoniae

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

Elongation factor Tu

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

9v5s__assembly_1__model_1

9v5s__assembly_1__model_1 | I(q)

9v5s__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

Crystal structure of EF-Tu from Mycoplasma pneumoniae

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

Elongation factor Tu

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

9v5s__assembly_1__model_1

9v5s__assembly_1__model_1 | I(q)

9v5s__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)