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1d2e

CRYSTAL STRUCTURE OF MITOCHONDRIAL EF-TU IN COMPLEX WITH GDP

Method: X-RAY DIFFRACTION Dmax: 149.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ELONGATION FACTOR TU (EF-TU)

OrganismNot specified

UniProt P49410

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 55–451 Chain B； UniProt 55–451 Chain C； UniProt 55–451 Chain D； UniProt 55–451 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

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 1D2E Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1XB2 Crystal Structure of Bos taurus mitochondrial Elongation Factor Tu/Ts Complex Deposited 2004-08-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 44–452（409 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule 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

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 1–397； UniProt 55–451 Author chain B； PDBConstruct 1–397； UniProt 55–451 Author chain C； PDBConstruct 1–397； UniProt 55–451 Author chain D； PDBConstruct 1–397； UniProt 55–451

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.

SAXS scattering curve SAXS Profile

SAXS profile for 1d2e

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1d2e
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1d2e
Deposition date deposition_date1999-09-23
Structure title titleCRYSTAL STRUCTURE OF MITOCHONDRIAL EF-TU IN COMPLEX WITH GDP
Keywords keywordsG-PROTEIN, BETA-BARREL, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier45.99 Å
Radius of gyration Rg (electron density) rg_electron45.98 Å
Forward intensity I(0) i0463360000.00
Molecular weight molecular_weight176760.0 kDa
Excluded volume excluded_volume221240 ų
Envelope volume envelope_volume305650 ų
Hydration-shell volume shell_volume56919 ų
Envelope diameter envelope_diameter155.0 Å
Shell Rg shell_rg48.92 Å
Envelope Rg envelope_rg44.71 Å
Shape Rg shape_rg45.97 Å
Total Rg total_rg46.13 Å
Total atoms total_atoms12396
Residues n_residues1588
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax149.1 Å
Rg (real space) rg_real46.22 Å
Rg uncertainty (real space) rg_real_error1.19 Å
I(0) (real space) i0_real4.6340e+08
I(0) uncertainty (real space) i0_real_error8.3320e+06
Rg (reciprocal space) rg_reciprocal46.00 Å
I(0) (reciprocal space) i0_reciprocal463200000.0000
Solution quality estimate total_estimate0.8142
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary43.8 Å
Skewness Skewness skewness0.365
Kurtosis Kurtosis kurtosis-0.648
Angular range angular_range— – 0.1700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha29370000.0000
Real-space data points n_real_points35
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.869; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd1d2ea1
Class classb — All beta proteins
Fold Fold foldb.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamilyb.43.3 — Translation proteins
Family Family familyb.43.3.1 — Elongation factors
Domain ID domain_idd1d2ea2
Class classb — All beta proteins
Fold Fold foldb.44 — Elongation factor/aminomethyltransferase common domain
Superfamily Superfamily superfamilyb.44.1 — EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain
Family Family familyb.44.1.1 — EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain
Domain ID domain_idd1d2ea3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.8 — G proteins
Domain ID domain_idd1d2eb1
Class classb — All beta proteins
Fold Fold foldb.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamilyb.43.3 — Translation proteins
Family Family familyb.43.3.1 — Elongation factors
Domain ID domain_idd1d2eb2
Class classb — All beta proteins
Fold Fold foldb.44 — Elongation factor/aminomethyltransferase common domain
Superfamily Superfamily superfamilyb.44.1 — EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain
Family Family familyb.44.1.1 — EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain
Domain ID domain_idd1d2eb3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.8 — G proteins
Domain ID domain_idd1d2ec1
Class classb — All beta proteins
Fold Fold foldb.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamilyb.43.3 — Translation proteins
Family Family familyb.43.3.1 — Elongation factors
Domain ID domain_idd1d2ec2
Class classb — All beta proteins
Fold Fold foldb.44 — Elongation factor/aminomethyltransferase common domain
Superfamily Superfamily superfamilyb.44.1 — EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain
Family Family familyb.44.1.1 — EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain
Domain ID domain_idd1d2ec3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.8 — G proteins
Domain ID domain_idd1d2ed1
Class classb — All beta proteins
Fold Fold foldb.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamilyb.43.3 — Translation proteins
Family Family familyb.43.3.1 — Elongation factors
Domain ID domain_idd1d2ed2
Class classb — All beta proteins
Fold Fold foldb.44 — Elongation factor/aminomethyltransferase common domain
Superfamily Superfamily superfamilyb.44.1 — EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain
Family Family familyb.44.1.1 — EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain
Domain ID domain_idd1d2ed3
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamilyc.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family familyc.37.1.8 — G proteins

CATH v4.4 (12 domains)

Domain ID domain_id1d2eA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id1d2eA02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily10 — Translation factors
Domain ID domain_id1d2eA03
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily10 — Translation factors
Domain ID domain_id1d2eB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id1d2eB02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily10 — Translation factors
Domain ID domain_id1d2eB03
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily10 — Translation factors
Domain ID domain_id1d2eC01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id1d2eC02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily10 — Translation factors
Domain ID domain_id1d2eC03
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily10 — Translation factors
Domain ID domain_id1d2eD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id1d2eD02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily10 — Translation factors
Domain ID domain_id1d2eD03
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily10 — Translation factors
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8. Citations (3)

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9. Files and Curves (10)