3cb4

The Crystal Structure of LepA

Method: X-RAY DIFFRACTION D_max: 168.1 Å Quality: GOOD

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

GTP-binding protein lepA

Escherichia coli

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 1–599	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；100 mM Tris-HCl pH 8.0 10% Peg 2000MME, 100 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.80 Å R-free 0.295
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–599	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；100 mM Tris-HCl pH 8.0 10% Peg 2000MME, 100 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.80 Å R-free 0.295
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1–599	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；100 mM Tris-HCl pH 8.0 10% Peg 2000MME, 100 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.80 Å R-free 0.295
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 1–599	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；100 mM Tris-HCl pH 8.0 10% Peg 2000MME, 100 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.80 Å R-free 0.295
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 1–599	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；100 mM Tris-HCl pH 8.0 10% Peg 2000MME, 100 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.80 Å R-free 0.295
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 1–599	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；100 mM Tris-HCl pH 8.0 10% Peg 2000MME, 100 mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.80 Å R-free 0.295

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 3CB4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3DEG Complex of elongating Escherichia coli 70S ribosome and EF4(LepA)-GMPPNP Deposited 2008-06-10	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: undecameric	Chain C 1–545（545 aa） Fragment：EF4	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 20 mM HEPES-KOH (pH 7.6), 4.5 mM Mg(CH3COO)2, 150 mM NH4CH3COO, 4 mM B-mercaptoethanol, 2 mM spermidine, and 0.05 mM spermine cryo-EM vitrification conditions Cryogen ETHANE	Resolution 10.90 Å
3JCD Structure of Escherichia coli EF4 in posttranslocational ribosomes (Post EF4) Deposited 2015-12-01	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 57-meric	Chain x 1–599（599 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
3JCE Structure of Escherichia coli EF4 in pretranslocational ribosomes (Pre EF4) Deposited 2015-12-01	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 58-meric	Chain x 1–599（599 aa）	Not recorded	PHE PHENYLALANINE × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LEPA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–599； UniProt 1–599 Author chain B； PDBConstruct 1–599； UniProt 1–599 Author chain C； PDBConstruct 1–599； UniProt 1–599 Author chain D； PDBConstruct 1–599； UniProt 1–599 Author chain E； PDBConstruct 1–599； UniProt 1–599 Author chain F； PDBConstruct 1–599； UniProt 1–599

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3cb4
Deposition date deposition_date	2008-02-21
Structure title title	The Crystal Structure of LepA
Keywords keywords	GTPAse, OB-fold, GTP-binding, Membrane, Nucleotide-binding, 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	52.60 Å
Radius of gyration Rg (electron density) rg_electron	52.27 Å
Forward intensity I(0) i0	1734370000.00
Molecular weight molecular_weight	348500.0 kDa
Excluded volume excluded_volume	437180 Å³
Envelope volume envelope_volume	658310 Å³
Hydration-shell volume shell_volume	106050 Å³
Envelope diameter envelope_diameter	172.6 Å
Shell Rg shell_rg	55.68 Å
Envelope Rg envelope_rg	50.27 Å
Shape Rg shape_rg	52.26 Å
Total Rg total_rg	52.43 Å
Total atoms total_atoms	24492
Residues n_residues	3150
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	168.1 Å
Rg (real space) rg_real	52.53 Å
Rg uncertainty (real space) rg_real_error	1.23 Å
I(0) (real space) i0_real	1.7340e+09
I(0) uncertainty (real space) i0_real_error	3.1810e+07
Rg (reciprocal space) rg_reciprocal	52.64 Å
I(0) (reciprocal space) i0_reciprocal	1735000000.0000
Solution quality estimate total_estimate	0.8484
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	61.6 Å
Skewness Skewness skewness	0.316
Kurtosis Kurtosis kurtosis	-0.354
Angular range angular_range	— – 0.1500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	126100000.0000
Real-space data points n_real_points	31
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.866; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.449

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	GTP-binding protein lepA
Molecular weight formula_weight	66652.1 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,A,B,C,E,F
Atom count atom_count	24495

MKNIRNFSIIAHIDHGKSTLSDRIIQICGGLSDREMEAQVLDSMDLERERGITIKAQSVTLDYKASDGETYQLNFIDTPGHVDFSYEVSRSLAACEGALLVVDAGQGVEAQTLANCYTAMEMDLEVVPVLNKIDLPAADPERVAEEIEDIVGIDATDAVRCSAKTGVGVQDVLERLVRDIPPPEGDPEGPLQALIIDSWFDNYLGVVSLIRIKNGTLRKGDKVKVMSTGQTYNADRLGIFTPKQVDRTELKCGEVGWLVCAIKDIHGAPVGDTLTLARNPAEKALPGFKKVKPQVYAGLFPVSSDDYEAFRDALGKLSLNDASLFYEPESSSALGFGFRCGFLGLLHMEIIQERLEREYDLDLITTAPTVVYEVETTSREVIYVDSPSKLPAVNNIYELREPIAECHMLLPQAYLGNVITLCVEKRGVQTNMVYHGNQVALTYEIPMAEVVLDFFDRLKSTSRGYASLDYNFKRFQASDMVRVDVLINGERVDALALITHRDNSQNRGRELVEKMKDLIPRQQFDIAIQAAIGTHIIARSTVKQLRKNVLAKCYGGDISRKKKLLQKQKEGKKRMKQIGNVELPQEAFLAILHVGKDNK

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	3

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7. Fold Classification (SCOP + CATH) 30 domains

CATH v4.4 (30 domains)

Domain ID domain_id	3cb4A01
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	3cb4A02
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	3cb4A03
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	3cb4A04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	240 —

Domain ID domain_id	3cb4A05
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	2570 — Elongation factor 4, C-terminal domain

Domain ID domain_id	3cb4B01
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	3cb4B02
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	3cb4B03
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	3cb4B04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	240 —

Domain ID domain_id	3cb4B05
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	2570 — Elongation factor 4, C-terminal domain

Domain ID domain_id	3cb4C01
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	3cb4C02
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	3cb4C03
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	3cb4C04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	240 —

Domain ID domain_id	3cb4C05
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	2570 — Elongation factor 4, C-terminal domain

Domain ID domain_id	3cb4D01
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	3cb4D02
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	3cb4D03
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	3cb4D04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	240 —

Domain ID domain_id	3cb4D05
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	2570 — Elongation factor 4, C-terminal domain

Domain ID domain_id	3cb4E01
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	3cb4E02
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	3cb4E03
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	3cb4E04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	240 —

Domain ID domain_id	3cb4E05
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	2570 — Elongation factor 4, C-terminal domain

Domain ID domain_id	3cb4F01
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	3cb4F02
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	3cb4F03
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	3cb4F04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	240 —

Domain ID domain_id	3cb4F05
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	2570 — Elongation factor 4, C-terminal domain

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8. Citations (1)

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Unit-cell length a length_a	97.960 Å
Unit-cell length b length_b	146.243 Å
Unit-cell length c length_c	139.317 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.60 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2490
R_work r_work	0.2464
R_free r_free	0.2945

fit	/app/data/saxs_computation/cb/3cb4/3cb4.fit
pddf	/app/data/pr_computation/cb/3cb4/3cb4.pr.out
profile	/app/data/saxs_computation/cb/3cb4/3cb4.dat