SAXSdb — 4m1k

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

Elongation factor G

Thermus thermophilus

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–691	Mutation：Q500L	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；5mM Tris-HCl (pH 7.6), 10mM MgCl2, 5mM GDP, 20-23% PEG8000, 0.1M Tris-Cl PH7.5-7.6, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.95 Å R-free 0.292

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 4M1K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EFG THE CRYSTAL STRUCTURE OF ELONGATION FACTOR G COMPLEXED WITH GDP, AT 2.7 ANGSTROMS RESOLUTION Deposited 1994-10-17	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–691（691 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；277 K；pH 7.8, temperature 277K	Resolution 2.70 Å R-free 0.396
1FNM STRUCTURE OF THERMUS THERMOPHILUS EF-G H573A Deposited 2000-08-22	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–691（691 aa）	Mutation：H573A	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；PEG 8000 (Fluka), guanosine 5'-diphophate, magnesium chloride , pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.80 Å R-free 0.295
1JQM Fitting of L11 protein and elongation factor G (EF-G) in the cryo-em map of e. coli 70S ribosome bound with EF-G, GDP and fusidic acid Deposited 2001-08-07	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–691（691 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6	Resolution 18.00 Å
1JQS Fitting of L11 protein and elongation factor G (domain G' and V) in the cryo-em map of E. coli 70S ribosome bound with EF-G and GMPPCP, a nonhydrolysable GTP analog Deposited 2001-08-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 220–251（32 aa） Fragment：;part of domain G' ; Chain C 606–673（68 aa） Fragment：domain V	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 18.00 Å
1KTV Crystal Structure of Elongation Factor G Dimer Without Nucleotide Deposited 2002-01-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–691（691 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；PEG 8000, HEPES, Tris, Dithiothreitol, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.80 Å R-free 0.374
1KTV Crystal Structure of Elongation Factor G Dimer Without Nucleotide Deposited 2002-01-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–691（691 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；PEG 8000, HEPES, Tris, Dithiothreitol, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.80 Å R-free 0.374
1PN6 Domain-wise fitting of the crystal structure of T.thermophilus EF-G into the low resolution map of the release complex.Puromycin.EFG.GDPNP of E.coli 70S ribosome. Deposited 2003-06-12	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–691（691 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Rapid-freezing in liquid ethane	Resolution 10.80 Å
2BCW Coordinates of the N-terminal domain of ribosomal protein L11,C-terminal domain of ribosomal protein L7/L12 and a portion of the G' domain of elongation factor G, as fitted into cryo-em map of an Escherichia coli 70SEF-GGDP*fusidic acid complex Deposited 2005-10-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 200–257（58 aa） Fragment：;A portion of G' domain' ;	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 20mM HEPES-KOH (pH 7.5), 6mM MgCl2, and 150 mM NH4Cl, 2mM spermidine, 0.4 mM spermine；pH 7.5；20mM HEPES-KOH (pH 7.5), 6mM MgCl2, and 150 mM NH4Cl, 2mM spermidine, 0.4 mM spermine cryo-EM vitrification conditions RAPID-FREEZING IN LIQUID ETHANE	Resolution 11.20 Å
2BM0 Ribosomal elongation factor G (EF-G) Fusidic acid resistant mutant T84A Deposited 2005-03-09	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–691（691 aa）	Mutation：YES	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.3；17% PEG 8000 100 MM HEPES 46 MM TRIS-HCL PH 7.3	Resolution 2.40 Å R-free 0.274
2BM1 Ribosomal elongation factor G (EF-G) Fusidic acid resistant mutant G16V Deposited 2005-03-09	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–691（691 aa）	Mutation：YES	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.3；17 % PEG8000 100 MM HEPES 46 MM TRIS-HCL PH 7.3 10 MM MAGNESIUM CHLORIDE	Resolution 2.60 Å R-free 0.297
2BV3 Crystal structure of a mutant elongation factor G trapped with a GTP analogue Deposited 2005-06-22	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–691（691 aa）	Mutation：YES	GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.3；17 % PEG8000, 10 MM MGCL2, 100 MM GDPNP, 46 MM TRIS, 100 MM HEPES, pH 7.30	Resolution 2.50 Å R-free 0.270
2EFG TRANSLATIONAL ELONGATION FACTOR G COMPLEXED WITH GDP Deposited 1998-09-23	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 1–691（691 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；18% W/V PEG8000, 20MM TRIS-HCL, 20MM AMMONIUM ACETATE, 2MM DTT, 1MM SODIUM AZIDE, 1MM GDP, pH 7.8, VAPOR DIFFUSION, HANGING DROP	Resolution 2.60 Å R-free 0.279
2J7K Crystal structure of the T84A mutant EF-G:GDPCP complex Deposited 2006-10-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–691（691 aa）	Mutation：YES	GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.3；17 % PEG8000 100 MM HEPES 46 MM TRIS 10 MM MGCL2 10 MM GDPCP, pH 7.3	Resolution 2.90 Å R-free 0.288
2OM7 Structural Basis for Interaction of the Ribosome with the Switch Regions of GTP-bound Elongation Factors Deposited 2007-01-21	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: tetradecameric	Chain L 1–691（691 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 0.3 mM GMPPNP, 10 mM Hepes-KOH (pH 7.8), 10 mM Mg acetate, 60 mM NH4Cl, and 6 mM B-mercaptoethanol；pH 7.8；0.3 mM GMPPNP, 10 mM Hepes-KOH (pH 7.8), 10 mM Mg acetate, 60 mM NH4Cl, and 6 mM B-mercaptoethanol cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.30 Å
3IZP Conformation of EF-G during translocation Deposited 2010-11-15	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 1–688（688 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；5 mM potassium phosphate, 5 mM magnesium acetate, 5 mM ammonium chloride, 95 mM potassium chloride, 0.5 mM calcium chloride, 8 mM putrescine, 1 mM spermidine, and 1 mM dithioerythritol cryo-EM vitrification conditions two-face blotting for 1 second；90 K；Cryogen ETHANE	Resolution not provided
4MYT Crystal structure of elongation factor G (EFG) Deposited 2013-09-28	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–691（691 aa）	Mutation：E579A	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；5 mM Tris-HCl (pH 7.6), 10mM MgCl2, 5mM GDP, 20-23% PEG 8000, 0.1M Tris-Cl (PH 7.5-7.6), VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 3.50 Å R-free 0.308
4MYU Crystal structure of elongation factor G mutant(EFG) Deposited 2013-09-28	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–691（691 aa）	Mutation：H573K	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；5mM Tris-HCl (pH 7.6), 10mM MgCl2, 5mM GDP, 20-23% PEG 8000, 0.1M Tris-Cl (PH 7.5-7.6), VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 3.00 Å R-free 0.271

16 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	EFG_THETH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–691； UniProt 1–691

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	4m1k
Deposition date deposition_date	2013-08-02
Structure title title	Crystal structure of elongation factor G (EFG)
Keywords keywords	Elongation factor G, 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	31.13 Å
Radius of gyration Rg (electron density) rg_electron	31.04 Å
Forward intensity I(0) i0	83258500.00
Molecular weight molecular_weight	72947.0 kDa
Excluded volume excluded_volume	91793 Å³
Envelope volume envelope_volume	117450 Å³
Hydration-shell volume shell_volume	33556 Å³
Envelope diameter envelope_diameter	118.1 Å
Shell Rg shell_rg	35.65 Å
Envelope Rg envelope_rg	31.04 Å
Shape Rg shape_rg	31.06 Å
Total Rg total_rg	31.40 Å
Total atoms total_atoms	5133
Residues n_residues	656
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	112.1 Å
Rg (real space) rg_real	31.38 Å
Rg uncertainty (real space) rg_real_error	1.34 Å
I(0) (real space) i0_real	8.3260e+07
I(0) uncertainty (real space) i0_real_error	1.4130e+06
Rg (reciprocal space) rg_reciprocal	31.28 Å
I(0) (reciprocal space) i0_reciprocal	83250000.0000
Solution quality estimate total_estimate	0.8267
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	35.2 Å
Skewness Skewness skewness	0.609
Kurtosis Kurtosis kurtosis	0.150
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15110000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.686; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.794; Smooth: 0.891

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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 G
Molecular weight formula_weight	76962.1 kDa
Mutation mutation	Q500L
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	5133

MAVKVEYDLKRLRNIGIAAHIDAGKTTTTERILYYTGRIHKIGEVHEGAATMDFMEQERERGITITAAVTTCFWKDHRINIIDTPGHVDFTIEVERSMRVLDGAIVVFDSSQGVEPQSETVWRQAEKYKVPRIAFANKMDKTGADLWLVIRTMQERLGARPVVMQLPIGREDTFSGIIDVLRMKAYTYGNDLGTDIREIPIPEEYLDQAREYHEKLVEVAADFDENIMLKYLEGEEPTEEELVAAIRKGTIDLKITPVFLGSALKNKGVQLLLDAVVDYLPSPLDIPPIKGTTPEGEVVEIHPDPNGPLAALAFKIMADPYVGRLTFIRVYSGTLTSGSYVYNTTKGRKERVARLLRMHANHREEVEELKAGDLGAVVGLKETITGDTLVGEDAPRVILESIEVPEPVIDVAIEPKTKADQEKLSQALARLAEEDPTFRVSTHPETGQTIISGMGELHLEIIVDRLKREFKVDANVGKPQVAYRETITKPVDVEGKFIRLTGGRGQYGHVKIKVEPLPRGSGFEFVNAIVGGVIPKEYIPAVQKGIEEAMQSGPLIGFPVVDIKVTLYDGSYHEVDSSEMAFKIAGSMAIKEAVQKGDPVILEPIMRVEVTTPEEYMGDVIGDLNARRGQILGMEPRGNAQVIRAFVPLAEMFGYATDLRSKTQGRGSFVMFFDHYQEVPKQVQEKLIKGQ

来源 Source

来源生物 organism	Thermus thermophilus
NCBI Class编号 ncbi_taxonomy_id	274
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	1

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7. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id	4m1kA01
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	4m1kA02
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	4m1kA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	870 — Elongation Factor G (Translational Gtpase), domain 3

Domain ID domain_id	4m1kA04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	230 — Ribosomal Protein S5; domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4m1kA05
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	240 —

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8. Citations (1)

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Unit-cell length a length_a	75.989 Å
Unit-cell length b length_b	86.767 Å
Unit-cell length c length_c	123.118 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.952 Å
Low-resolution limit resolution_low	37.995 Å
R factor r_factor	0.1985
R_work r_work	0.1936
R_free r_free	0.2919

fit	/app/data/saxs_computation/m1/4m1k/4m1k.fit
pddf	/app/data/pr_computation/m1/4m1k/4m1k.pr.out
profile	/app/data/saxs_computation/m1/4m1k/4m1k.dat

Crystal structure of elongation factor G (EFG)

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

Elongation factor G

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