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1bam

STRUCTURE OF RESTRICTION ENDONUCLEASE BAMHI PHASED AT 1.95 ANGSTROMS RESOLUTION BY MAD ANALYSIS

Method: X-RAY DIFFRACTION Dmax: 58.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ENDONUCLEASE BamH I

Bacillus amyloliquefaciens

UniProt P23940

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 1–213 Not recorded No other associated polymer X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.95 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 1BAM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BHM RESTRICTION ENDONUCLEASE BAMHI COMPLEX WITH DNA Deposited 1995-07-12 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 1–213（213 aa）
Chain B 1–213（213 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.20 Å
1ESG RESTRICTION ENDONUCLEASE BAMHI BOUND TO A NON-SPECIFIC DNA. Deposited 2000-04-09 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 1–213（213 aa）
Chain B 1–213（213 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；293 K；30% MPD, 10 mM sodium acetate (pH 4.8), 5 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Resolution 1.90 Å R-free 0.230
2BAM RESTRICTION ENDONUCLEASE BAMHI COMPLEX WITH DNA AND CALCIUM IONS (PRE-REACTIVE COMPLEX). Deposited 1998-08-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: tetrameric
Chain A 1–213（213 aa）
Chain B 1–213（213 aa）
Not recorded CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.3；12-14% PEG8000, 0.1M MES (PH 5.3), 0.15M KCL, 5% GLYCEROL
Resolution 2.00 Å R-free 0.251
3BAM RESTRICTION ENDONUCLEASE BAMHI COMPLEX WITH DNA AND MANGANESE IONS (POST-REACTIVE COMPLEX) Deposited 1998-08-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 2 PDB declaration: pentameric
Chain A 1–213（213 aa）
Chain B 1–213（213 aa）
Not recorded MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.3；pH 5.3 CATALYSIS OCCURRED IN THE CRYSTAL AFTER SOAKING MANGANESE ION. THE ACTIVE SITE OF THE R SUBUNIT CLEAVED THE ORIGINAL D STRAND IN TWO (D AND E) RESULTING IN A POST-REACTIVE COMPLEX.
Resolution 1.80 Å R-free 0.268

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name T2BA_BACAM
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–213； UniProt 1–213

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 1bam

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1bam
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1bam
Deposition date deposition_date1994-12-28
Structure title titleSTRUCTURE OF RESTRICTION ENDONUCLEASE BAMHI PHASED AT 1.95 ANGSTROMS RESOLUTION BY MAD ANALYSIS
Keywords keywordsENDONUCLEASE; ENDONUCLEASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier18.02 Å
Radius of gyration Rg (electron density) rg_electron16.66 Å
Forward intensity I(0) i09191820.00
Molecular weight molecular_weight22998.0 kDa
Excluded volume excluded_volume29043 ų
Envelope volume envelope_volume32597 ų
Hydration-shell volume shell_volume16381 ų
Envelope diameter envelope_diameter59.9 Å
Shell Rg shell_rg22.77 Å
Envelope Rg envelope_rg16.98 Å
Shape Rg shape_rg16.65 Å
Total Rg total_rg17.72 Å
Total atoms total_atoms1619
Residues n_residues200
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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax58.7 Å
Rg (real space) rg_real17.92 Å
Rg uncertainty (real space) rg_real_error0.42 Å
I(0) (real space) i0_real9.1920e+06
I(0) uncertainty (real space) i0_real_error1.2350e+05
Rg (reciprocal space) rg_reciprocal17.94 Å
I(0) (reciprocal space) i0_reciprocal9192000.0000
Solution quality estimate total_estimate0.8058
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary23.0 Å
Skewness Skewness skewness0.214
Kurtosis Kurtosis kurtosis-0.328
Angular range angular_range— – 0.4400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1847000.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.825; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; 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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1bama_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.52 — Restriction endonuclease-like
Superfamily Superfamily superfamilyc.52.1 — Restriction endonuclease-like
Family Family familyc.52.1.3 — Restriction endonuclease BamHI

CATH v4.4 (1 domains)

Domain ID domain_id1bamA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology91 — Restriction Endonuclease
Homologous superfamily homologous superfamily20 —
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8. Citations (2)

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9. Files and Curves (10)