SAXSdb — 5m04

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

GTPase ObgE/CgtA

Escherichia coli DH5[alpha]

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	OBG_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–360； UniProt 1–340

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	5m04
Deposition date deposition_date	2016-10-03
Structure title title	Structure of ObgE from Escherichia coli
Keywords keywords	GTPase, ObgE, CgtA, hydrolase; HYDROLASE
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.

5m04__assembly_1__model_1

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

Download this curve (.dat)

5m04__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5m04__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.84 Å
Rg (electron density)	28.86 Å
Total Rg	28.94 Å
Atom count	2599
Residues	337
Excluded volume	46195 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5m04__assembly_1__model_1`	monomeric （1）	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	GTPase ObgE/CgtA
Molecular weight formula_weight	39198.7 kDa
EC 编号 ec_number	3.6.5.-
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	2776

MGSSHHHHHHSSGLVPRGSHMKFVDEASILVVAGDGGNGCVSFRREKYIPKGGPDGGDGGDGGDVWMEADENLNTLIDYRFEKSFRAERGQNGASRDCTGKRGKDVTIKVPVGTRVIDQGTGETMGDMTKHGQRLLVAKGGWHGLGNTRFKSSVNRTPRQKTNGTPGDKRELLLELMLLADVGMLGMPNAGKSTFIRAVSAAKPKVADYPFTTLVPSLGVVRMDNEKSFVVADIPGLIEGAAEGAGLGIRFLKHLERCRVLLHLIDIDPIDGTDPVENARIIISELEKYSQDLATKPRWLVFNKIDLLDKVEAEEKAKAIAEALGWEDKYYLISAASGLGVKDLCWDVMTFIIENPVVQA

Source Source

Source organism organism	Escherichia coli DH5[alpha]
NCBI taxonomy ID ncbi_taxonomy_id	668369
Host organism host_organism	Escherichia coli BL21(DE3)

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	1

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	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	169

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5m04A01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	210 — Spo0b-associated Gtp-binding Protein; Chain: A,
Homologous superfamily homologous superfamily	12 — GTP1/OBG domain

Domain ID domain_id	5m04A02
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

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Unit-cell length a length_a	64.590 Å
Unit-cell length b length_b	83.000 Å
Unit-cell length c length_c	177.460 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	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	88.730 Å
R factor r_factor	0.2001
R_work r_work	0.1980
R_free r_free	0.2388

Structure of ObgE from Escherichia coli

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

GTPase ObgE/CgtA

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

5m04__assembly_1__model_1

5m04__assembly_1__model_1 | I(q)

5m04__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

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Structure of ObgE from Escherichia coli

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

GTPase ObgE/CgtA

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

5m04__assembly_1__model_1

5m04__assembly_1__model_1 | I(q)

5m04__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

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)