← Back to search
1cbf

THE X-RAY STRUCTURE OF A COBALAMIN BIOSYNTHETIC ENZYME, COBALT PRECORRIN-4 METHYLTRANSFERASE, CBIF

Method: X-RAY DIFFRACTION Dmax: 69.3 Å Quality: REASONABLE
▼

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

COBALT-PRECORRIN-4 TRANSMETHYLASE

Bacillus megaterium

UniProt O87696

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 1–242 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

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 1CBF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2CBF THE X-RAY STRUCTURE OF A COBALAMIN BIOSYNTHETIC ENZYME, COBALT PRECORRIN-4 METHYLTRANSFERASE, CBIF, FROM BACILLUS MEGATERIUM, WITH THE HIS-TAG CLEAVED OFF 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 1–231（231 aa）
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

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 21–259； UniProt 1–242

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

SAXS profile for 1cbf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1cbf
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1cbf
Deposition date deposition_date1998-05-01
Structure title titleTHE X-RAY STRUCTURE OF A COBALAMIN BIOSYNTHETIC ENZYME, COBALT PRECORRIN-4 METHYLTRANSFERASE, CBIF
Keywords keywordsPRECORRIN-4 METHYLTRANSFERASE, METHYLASE, COBALAMIN BIOSYNTHESIS, METHYLTRANSFERASE; METHYLTRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.09 Å
Radius of gyration Rg (electron density) rg_electron20.14 Å
Forward intensity I(0) i012217800.00
Molecular weight molecular_weight26551.0 kDa
Excluded volume excluded_volume33478 ų
Envelope volume envelope_volume40131 ų
Hydration-shell volume shell_volume17309 ų
Envelope diameter envelope_diameter73.1 Å
Shell Rg shell_rg25.74 Å
Envelope Rg envelope_rg20.36 Å
Shape Rg shape_rg20.14 Å
Total Rg total_rg20.96 Å
Total atoms total_atoms1854
Residues n_residues239
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax69.3 Å
Rg (real space) rg_real21.15 Å
Rg uncertainty (real space) rg_real_error0.50 Å
I(0) (real space) i0_real1.2220e+07
I(0) uncertainty (real space) i0_real_error1.5630e+05
Rg (reciprocal space) rg_reciprocal21.14 Å
I(0) (reciprocal space) i0_reciprocal12220000.0000
Solution quality estimate total_estimate0.6543
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.4 Å
Skewness Skewness skewness0.385
Kurtosis Kurtosis kurtosis-0.470
Angular range angular_range— – 0.3750 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3090000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.825; Stabil: 1.000; Sysdev: 0.368; Positv: 1.000; Valcen: 0.925; Smooth: 0.000
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1cbfa1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.90 — Tetrapyrrole methylase
Superfamily Superfamily superfamilyc.90.1 — Tetrapyrrole methylase
Family Family familyc.90.1.1 — Tetrapyrrole methylase
Domain ID domain_idd1cbfa2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id1cbfA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1010 — Cobalt-precorrin-4 Transmethylase; domain 1
Homologous superfamily homologous superfamily10 — Tetrapyrrole methylase, N-terminal domain
Domain ID domain_id1cbfA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology950 — Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2
Homologous superfamily homologous superfamily10 — Tetrapyrrole methylase, C-terminal domain
▶

8. Citations (2)

▶

9. Files and Curves (10)