SAXSdb — 1cbu

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

ADENOSYLCOBINAMIDE KINASE/ADENOSYLCOBINAMIDE PHOSPHATE GUANYLYLTRANSFERASE

Salmonella typhimurium

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 2–181 Chain B； UniProt 2–181 Chain C； UniProt 2–181	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：MICROBATCH；pH 5.5；PROTEIN WAS CRYSTALLIZED BY MICRO BATCH FROM 6% PEG 3350, 200 MM NACL AND 50 MM SUCCINATE, PH 5.5 AT 4 C., micro batch	Resolution 2.30 Å

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 1CBU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C9K THE THREE DIMENSIONAL STRUCTURE OF ADENOSYLCOBINAMIDE KINASE/ ADENOSYLCOBINAMIDE PHOSPHATE GUALYLYLTRANSFERASE (COBU) COMPLEXED WITH GMP: EVIDENCE FOR A SUBSTRATE INDUCED TRANSFERASE ACTIVE SITE Deposited 1999-08-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 2–181（180 aa） Chain B 2–181（180 aa） Chain C 2–181（180 aa）	Not recorded	PO4 PHOSPHATE ION × 2 5GP GUANOSINE-5'-MONOPHOSPHATE × 3 MG MAGNESIUM ION × 1 POP PYROPHOSPHATE 2- × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH；pH 9；277 K；16% PEG 4000 100 MM CACL2 50 MM CHES, pH 9.0, BATCH	Resolution 2.20 Å

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

View Construct and Data Evidence

UniProt name	COBU_SALTY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–180； UniProt 2–181 Author chain B； PDBConstruct 1–180； UniProt 2–181 Author chain C； PDBConstruct 1–180； UniProt 2–181

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	1cbu
Deposition date deposition_date	1998-03-12
Structure title title	ADENOSYLCOBINAMIDE KINASE/ADENOSYLCOBINAMIDE PHOSPHATE GUANYLYLTRANSFERASE (COBU) FROM SALMONELLA TYPHIMURIUM
Keywords keywords	COBALAMIN BIOSYNTHESIS, ADENOSYLCOBINAMIDE, KINASE, ATPASE, GUANYLYLTRANSFERASE, SALMONELLA TYPHIMURIUM, TRANSFERASE, COENZYME B12; COBALAMIN BIOSYNTHESIS
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	26.13 Å
Radius of gyration Rg (electron density) rg_electron	24.81 Å
Forward intensity I(0) i0	60843700.00
Molecular weight molecular_weight	58986.0 kDa
Excluded volume excluded_volume	73296 Å³
Envelope volume envelope_volume	90797 Å³
Hydration-shell volume shell_volume	30253 Å³
Envelope diameter envelope_diameter	81.2 Å
Shell Rg shell_rg	32.43 Å
Envelope Rg envelope_rg	24.94 Å
Shape Rg shape_rg	24.87 Å
Total Rg total_rg	25.48 Å
Total atoms total_atoms	4132
Residues n_residues	539
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	77.8 Å
Rg (real space) rg_real	26.00 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	6.0840e+07
I(0) uncertainty (real space) i0_real_error	8.3890e+05
Rg (reciprocal space) rg_reciprocal	26.04 Å
I(0) (reciprocal space) i0_reciprocal	60850000.0000
Solution quality estimate total_estimate	0.9125
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.9 Å
Skewness Skewness skewness	0.154
Kurtosis Kurtosis kurtosis	-0.541
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11990000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.969; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.960

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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	ADENOSYLCOBINAMIDE KINASE/ADENOSYLCOBINAMIDE PHOSPHATE GUANYLYLTRANSFERASE
Molecular weight formula_weight	19794.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	4334

MILVTGGARSGKSRHAEALIGDAPQVLYIATSQILDDEMAARIQHHKDGRPAHWRTAECWRHLDTLITADLAPDDAILLECITTMVTNLLFALGGENDPEQWDYAAMERAIDDEIQILIAACQRCPAKVVLVTNEVGMGIVPENRLARHFRDIAGRVNQRLAAAADEVWLVVSGIGVKIK

来源 Source

来源生物 organism	Salmonella typhimurium
NCBI Class编号 ncbi_taxonomy_id	602
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	202

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1cbua_
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.37.1.11 — RecA protein-like (ATPase-domain)

Domain ID domain_id	d1cbub_
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.37.1.11 — RecA protein-like (ATPase-domain)

Domain ID domain_id	d1cbuc_
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.37.1.11 — RecA protein-like (ATPase-domain)

CATH v4.4 (3 domains)

Domain ID domain_id	1cbuA00
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	1cbuB00
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	1cbuC00
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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8. Citations (2)

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Unit-cell length a length_a	96.400 Å
Unit-cell length b length_b	114.400 Å
Unit-cell length c length_c	106.700 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	24

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/cb/1cbu/1cbu.fit
pddf	/app/data/pr_computation/cb/1cbu/1cbu.pr.out
profile	/app/data/saxs_computation/cb/1cbu/1cbu.dat

ADENOSYLCOBINAMIDE KINASE/ADENOSYLCOBINAMIDE PHOSPHATE GUANYLYLTRANSFERASE (COBU) FROM SALMONELLA TYPHIMURIUM

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

ADENOSYLCOBINAMIDE KINASE/ADENOSYLCOBINAMIDE PHOSPHATE GUANYLYLTRANSFERASE

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