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1bhm

RESTRICTION ENDONUCLEASE BAMHI COMPLEX WITH DNA

Method: X-RAY DIFFRACTION Dmax: 74.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PROTEIN (BAMHI (E.C.3.1.21.4))

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–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain A； UniProt 1–213 Chain B； UniProt 1–213 Not recorded ;DNA (5'-D(*TP*AP*TP*GP*GP*AP*TP*CP*CP*AP*TP*A)-3') ; × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP Resolution 2.20 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 1BHM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BAM STRUCTURE OF RESTRICTION ENDONUCLEASE BAMHI PHASED AT 1.95 ANGSTROMS RESOLUTION BY MAD ANALYSIS Deposited 1994-12-28 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–213（213 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.95 Å
1ESG RESTRICTION ENDONUCLEASE BAMHI BOUND TO A NON-SPECIFIC DNA. Deposited 2000-04-09 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 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 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 2
Chains and sequence ranges Author chain A； PDBConstruct 1–213； UniProt 1–213 Author chain B； 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 1bhm

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1bhm
Deposition date deposition_date1995-07-12
Structure title titleRESTRICTION ENDONUCLEASE BAMHI COMPLEX WITH DNA
Keywords keywordsHYDROLASE, COMPLEX (ENDONUCLEASE-DNA), NUCLEASE, HYDROLASE-DNA COMPLEX; HYDROLASE/DNA
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_guinier22.88 Å
Radius of gyration Rg (electron density) rg_electron22.27 Å
Forward intensity I(0) i050350300.00
Molecular weight molecular_weight52499.0 kDa
Excluded volume excluded_volume64409 ų
Envelope volume envelope_volume73775 ų
Hydration-shell volume shell_volume27223 ų
Envelope diameter envelope_diameter79.8 Å
Shell Rg shell_rg29.77 Å
Envelope Rg envelope_rg22.54 Å
Shape Rg shape_rg22.29 Å
Total Rg total_rg23.03 Å
Total atoms total_atoms3671
Residues n_residues429
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 dmax74.6 Å
Rg (real space) rg_real22.80 Å
Rg uncertainty (real space) rg_real_error0.46 Å
I(0) (real space) i0_real5.0350e+07
I(0) uncertainty (real space) i0_real_error6.2750e+05
Rg (reciprocal space) rg_reciprocal22.82 Å
I(0) (reciprocal space) i0_reciprocal50350000.0000
Solution quality estimate total_estimate0.8068
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary73.4 Å
Skewness Skewness skewness0.299
Kurtosis Kurtosis kurtosis-0.272
Angular range angular_range— – 0.3450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11940000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.829; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1bhma_
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
Domain ID domain_idd1bhmb_
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 (2 domains)

Domain ID domain_id1bhmA00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology91 — Restriction Endonuclease
Homologous superfamily homologous superfamily20 —
Domain ID domain_id1bhmB00
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology91 — Restriction Endonuclease
Homologous superfamily homologous superfamily20 —
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8. Citations (1)

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9. Files and Curves (10)