2cbf

THE X-RAY STRUCTURE OF A COBALAMIN BIOSYNTHETIC ENZYME, COBALT PRECORRIN-4 METHYLTRANSFERASE, CBIF, FROM BACILLUS MEGATERIUM, WITH THE HIS-TAG CLEAVED OFF

Method: X-RAY DIFFRACTION D_max: 70.1 Å Quality: GOOD

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

COBALT-PRECORRIN-4 TRANSMETHYLASE

Bacillus megaterium

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–231	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；pH 8.5	Resolution 3.10 Å R-free 0.281

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 2CBF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CBF THE X-RAY STRUCTURE OF A COBALAMIN BIOSYNTHETIC ENZYME, COBALT PRECORRIN-4 METHYLTRANSFERASE, CBIF Deposited 1998-05-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–242（242 aa）	Mutation：HIS-TAGGED	PO4 PHOSPHATE ION × 4 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.40 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	CBIF_BACME
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–234； UniProt 1–231

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	2cbf
Deposition date deposition_date	1998-05-01
Structure title title	THE X-RAY STRUCTURE OF A COBALAMIN BIOSYNTHETIC ENZYME, COBALT PRECORRIN-4 METHYLTRANSFERASE, CBIF, FROM BACILLUS MEGATERIUM, WITH THE HIS-TAG CLEAVED OFF
Keywords keywords	PRECORRIN-4 METHYLTRANSFERASE, METHYLASE, COBALAMIN BIOSYNTHESIS, METHYLTRANSFERASE; METHYLTRANSFERASE
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	20.67 Å
Radius of gyration Rg (electron density) rg_electron	19.65 Å
Forward intensity I(0) i0	11345100.00
Molecular weight molecular_weight	25837.0 kDa
Excluded volume excluded_volume	32711 Å³
Envelope volume envelope_volume	38522 Å³
Hydration-shell volume shell_volume	16991 Å³
Envelope diameter envelope_diameter	65.4 Å
Shell Rg shell_rg	25.08 Å
Envelope Rg envelope_rg	19.67 Å
Shape Rg shape_rg	19.65 Å
Total Rg total_rg	20.47 Å
Total atoms total_atoms	1807
Residues n_residues	234
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	70.1 Å
Rg (real space) rg_real	20.69 Å
Rg uncertainty (real space) rg_real_error	0.64 Å
I(0) (real space) i0_real	1.1350e+07
I(0) uncertainty (real space) i0_real_error	1.4730e+05
Rg (reciprocal space) rg_reciprocal	20.69 Å
I(0) (reciprocal space) i0_reciprocal	11350000.0000
Solution quality estimate total_estimate	0.7881
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	20.3 Å
Skewness Skewness skewness	0.342
Kurtosis Kurtosis kurtosis	-0.539
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3312000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.783; Stabil: 0.985; Sysdev: 1.000; Positv: 1.000; Valcen: 0.938; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2cbfa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.90 — Tetrapyrrole methylase
Superfamily Superfamily superfamily	c.90.1 — Tetrapyrrole methylase
Family Family family	c.90.1.1 — Tetrapyrrole methylase

Domain ID domain_id	d2cbfa2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	2cbfA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1010 — Cobalt-precorrin-4 Transmethylase; domain 1
Homologous superfamily homologous superfamily	10 — Tetrapyrrole methylase, N-terminal domain

Domain ID domain_id	2cbfA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2
Homologous superfamily homologous superfamily	10 — Tetrapyrrole methylase, C-terminal domain

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8. Citations (2)

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Unit-cell length a length_a	80.040 Å
Unit-cell length b length_b	80.040 Å
Unit-cell length c length_c	77.960 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1830
R_free r_free	0.2810

Description description	COBALT-PRECORRIN-4 TRANSMETHYLASE
Molecular weight formula_weight	25504.8 kDa
EC 编号 ec_number	2.1.1.133
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1807

THE X-RAY STRUCTURE OF A COBALAMIN BIOSYNTHETIC ENZYME, COBALT PRECORRIN-4 METHYLTRANSFERASE, CBIF, FROM BACILLUS MEGATERIUM, WITH THE HIS-TAG CLEAVED OFF

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

COBALT-PRECORRIN-4 TRANSMETHYLASE

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Bacillus megaterium
NCBI Class编号 ncbi_taxonomy_id	1404
宿主生物 host_organism	Escherichia coli

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	syn
Copy count entity_count	1

fit	/app/data/saxs_computation/cb/2cbf/2cbf.fit
pddf	/app/data/pr_computation/cb/2cbf/2cbf.pr.out
profile	/app/data/saxs_computation/cb/2cbf/2cbf.dat