SAXSdb — 1xb2

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

Elongation factor Tu, mitochondrial

Bos taurus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 44–452	Non-standard monomer：Yes (specific site not provided by mmCIF)	Elongation factor Ts, mitochondrial × 1 （P43896）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.6；279 K；14-18% PEG 8000, 100 mM Tris-HCl pH 7.6, 200 mM Na3Citrate-2H2O, 2 mM DTT and 1 mM NaN3 , VAPOR DIFFUSION, SITTING DROP, temperature 279K	Resolution 2.20 Å R-free 0.247

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1XB2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D2E CRYSTAL STRUCTURE OF MITOCHONDRIAL EF-TU IN COMPLEX WITH GDP Deposited 1999-09-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 55–451（397 aa） Chain B 55–451（397 aa） Chain C 55–451（397 aa） Chain D 55–451（397 aa）	Not recorded	MG MAGNESIUM ION × 4 GDP GUANOSINE-5'-DIPHOSPHATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；277 K；MME 2K, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 4K	Resolution 1.94 Å R-free 0.257

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	EFTU_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–409； UniProt 44–452

Elongation factor Ts, mitochondrial

Bos taurus

UniProt P43896

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 56–338	Not recorded	Elongation factor Tu, mitochondrial × 1 （P49410）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.6；279 K；14-18% PEG 8000, 100 mM Tris-HCl pH 7.6, 200 mM Na3Citrate-2H2O, 2 mM DTT and 1 mM NaN3 , VAPOR DIFFUSION, SITTING DROP, temperature 279K	Resolution 2.20 Å R-free 0.247

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	EFTS_BOVIN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–283； UniProt 56–338

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	1xb2
Deposition date deposition_date	2004-08-27
Structure title title	Crystal Structure of Bos taurus mitochondrial Elongation Factor Tu/Ts Complex
Keywords keywords	Protein-protein complex, TRANSLATION; TRANSLATION
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	30.20 Å
Radius of gyration Rg (electron density) rg_electron	29.55 Å
Forward intensity I(0) i0	82797000.00
Molecular weight molecular_weight	71241.0 kDa
Excluded volume excluded_volume	88965 Å³
Envelope volume envelope_volume	113530 Å³
Hydration-shell volume shell_volume	32521 Å³
Envelope diameter envelope_diameter	99.8 Å
Shell Rg shell_rg	36.16 Å
Envelope Rg envelope_rg	29.49 Å
Shape Rg shape_rg	29.54 Å
Total Rg total_rg	30.17 Å
Total atoms total_atoms	4964
Residues n_residues	634
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	96.0 Å
Rg (real space) rg_real	30.18 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	8.2800e+07
I(0) uncertainty (real space) i0_real_error	1.2470e+06
Rg (reciprocal space) rg_reciprocal	30.19 Å
I(0) (reciprocal space) i0_reciprocal	82800000.0000
Solution quality estimate total_estimate	0.9047
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	35.1 Å
Skewness Skewness skewness	0.246
Kurtosis Kurtosis kurtosis	-0.584
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13770000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.952; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.916

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Elongation factor Tu, mitochondrial
Molecular weight formula_weight	45658.7 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	5294

AVEAKKTYVRDKPHVNVGTIGHVDHGKTTLTAAITKILAEGGGAKFKKYEEIDNAPEERARGITINAAHVEYSTAARHYAHTDCPGHADYVKNMITGTAPLDGCILVVAANDGPMPQTREHLLLARQIGVEHVVVYVNKADAVQDSEMVELVELEIRELLTEFGYKGEETPIIVGSALCALEQRDPELGLKSVQKLLDAVDTYIPVPTRDLEKPFLLPVESVYSIPGRGTVVTGTLERGILKKGDECEFLGHSKNIRTVVTGIEMFHKSLDRAEAGDNLGALVRGLKREDLRRGLVMAKPGSIQPHQKVEAQVYILTKEEGGRHKPFVSHFMPVMFSLTWDMACRIILPPGKELAMPGEDLKLTLILRQPMILEKGQRFTLRDGNRTIGTGLVTDTPAMTEEDKNIKWS

来源 Source

来源生物 organism	Bos taurus
通用名 common_name	cattle
NCBI Class编号 ncbi_taxonomy_id	9913
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Elongation factor Ts, mitochondrial
Molecular weight formula_weight	31849.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SASSKELLMKLRRKTGYSFINCKKALETCGGDLKQAESWLHKQAQKEGWSKAARLHGRKTKEGLIGLLQEGDTTVLVEVNCETDFVSRNLKFQQLVQQVALGTLLHCQNLKDQLSTYSKGFLNSSELSELPAGPEREGSLKDQLALAIGKLGENMILKRAAWVKVPAGFYVGSYVHGAMHSPSLHNLVLGKYGALVICETSELKANLADLGRRLGQHVVGMAPLSVGSLDDEPGGEAETKMLSQPYLLDPSITLGQYVQPHGVSVVDFVRFECGEGEDAADAELEHHHHHH

来源 Source

来源生物 organism	Bos taurus
通用名 common_name	cattle
NCBI Class编号 ncbi_taxonomy_id	9913
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	322

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1xb2a1
Class class	b — All beta proteins
Fold Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamily	b.43.3 — Translation proteins
Family Family family	b.43.3.1 — Elongation factors

Domain ID domain_id	d1xb2a2
Class class	b — All beta proteins
Fold Fold fold	b.44 — Elongation factor/aminomethyltransferase common domain
Superfamily Superfamily superfamily	b.44.1 — EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain
Family Family family	b.44.1.1 — EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain

Domain ID domain_id	d1xb2a3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.8 — G proteins

Domain ID domain_id	d1xb2b1
Class class	a — All alpha proteins
Fold Fold fold	a.5 — RuvA C-terminal domain-like
Superfamily Superfamily superfamily	a.5.2 — UBA-like
Family Family family	a.5.2.2 — TS-N domain

Domain ID domain_id	d1xb2b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.43 — EF-Ts domain-like
Superfamily Superfamily superfamily	d.43.1 — Elongation factor Ts (EF-Ts), dimerisation domain
Family Family family	d.43.1.1 — Elongation factor Ts (EF-Ts), dimerisation domain

Domain ID domain_id	d1xb2b3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.43 — EF-Ts domain-like
Superfamily Superfamily superfamily	d.43.1 — Elongation factor Ts (EF-Ts), dimerisation domain
Family Family family	d.43.1.1 — Elongation factor Ts (EF-Ts), dimerisation domain

CATH v4.4 (6 domains)

Domain ID domain_id	1xb2A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1xb2A02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	1xb2A03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	10 — Translation factors

Domain ID domain_id	1xb2B01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	10 — Ubiquitin-associated (UBA) domain

Domain ID domain_id	1xb2B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	479 — Tetrahydropterin Synthase; Chain A
Homologous superfamily homologous superfamily	20 — Elongation factor Ts, dimerisation domain

Domain ID domain_id	1xb2B03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	479 — Tetrahydropterin Synthase; Chain A
Homologous superfamily homologous superfamily	20 — Elongation factor Ts, dimerisation domain

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8. Citations (1)

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Unit-cell length a length_a	94.000 Å
Unit-cell length b length_b	149.300 Å
Unit-cell length c length_c	70.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	125.20 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2190
R_work r_work	0.2180
R_free r_free	0.2470

fit	/app/data/saxs_computation/xb/1xb2/1xb2.fit
pddf	/app/data/pr_computation/xb/1xb2/1xb2.pr.out
profile	/app/data/saxs_computation/xb/1xb2/1xb2.dat

Crystal Structure of Bos taurus mitochondrial Elongation Factor Tu/Ts Complex

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

Elongation factor Tu, mitochondrial

State in the Current Structure

Other States of the Same Protein in the Database

Elongation factor Ts, mitochondrial

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)