SAXSdb — 3bam

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

PROTEIN (RESTRICTION ENDONUCLEASE BAMHI)

Bacillus amyloliquefaciens

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 3 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain A； UniProt 1–213 Chain B； UniProt 1–213	Not recorded	;DNA (5'-D(TPAPTPGPGPAPTPCPCPAPTPA)-3') ; × 1 ;DNA (5'-D(TPAPTPG)-3') ; × 1 ;DNA (5'-D(PGPAPTPCPCPAPTPA)-3') ; × 1 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

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 3BAM	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 ligand/ion 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
1BHM RESTRICTION ENDONUCLEASE BAMHI COMPLEX WITH DNA Deposited 1995-07-12	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	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 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	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 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

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	4
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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3bam
Deposition date deposition_date	1998-08-19
Structure title title	RESTRICTION ENDONUCLEASE BAMHI COMPLEX WITH DNA AND MANGANESE IONS (POST-REACTIVE COMPLEX)
Keywords keywords	HYDROLASE, PHOSPHODIESTERASE, COMPLEX (ENDONUCLEASE-DNA), NUCLEASE, PROTEIN/DNA, HYDROLASE-DNA COMPLEX; HYDROLASE/DNA
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	22.87 Å
Radius of gyration Rg (electron density) rg_electron	22.34 Å
Forward intensity I(0) i0	53653900.00
Molecular weight molecular_weight	54807.0 kDa
Excluded volume excluded_volume	67538 Å³
Envelope volume envelope_volume	76826 Å³
Hydration-shell volume shell_volume	28008 Å³
Envelope diameter envelope_diameter	78.4 Å
Shell Rg shell_rg	30.11 Å
Envelope Rg envelope_rg	22.72 Å
Shape Rg shape_rg	22.35 Å
Total Rg total_rg	23.12 Å
Total atoms total_atoms	3825
Residues n_residues	438
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	74.3 Å
Rg (real space) rg_real	22.80 Å
Rg uncertainty (real space) rg_real_error	0.48 Å
I(0) (real space) i0_real	5.3650e+07
I(0) uncertainty (real space) i0_real_error	7.8500e+05
Rg (reciprocal space) rg_reciprocal	22.82 Å
I(0) (reciprocal space) i0_reciprocal	53650000.0000
Solution quality estimate total_estimate	0.8076
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.4 Å
Skewness Skewness skewness	0.305
Kurtosis Kurtosis kurtosis	-0.267
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13430000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.833; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(TPAPTPGPGPAPTPCPCPAPTPA)-3') ;
Molecular weight formula_weight	3661.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C
Atom count atom_count	4177

TATGGATCCATA

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(TPAPTPG)-3') ;
Molecular weight formula_weight	1205.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

TATG

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(PGPAPTPCPCPAPTPA)-3') ;
Molecular weight formula_weight	2410.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E

GATCCATA

Entity 4 Entity 4 polymer

Description description	PROTEIN (RESTRICTION ENDONUCLEASE BAMHI)
Molecular weight formula_weight	24602.3 kDa
EC 编号 ec_number	3.1.21.4
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

MEVEKEFITDEAKELLSKDKLIQQAYNEVKTSICSPIWPATSKTFTINNTEKNCNGVVPIKELCYTLLEDTYNWYREKPLDILKLEKKKGGPIDVYKEFIENSELKRVGMEFETGNISSAHRSMNKLLLGLKHGEIDLAIILMPIKQLAYYLTDRVTNFEELEPYFELTEGQPFIFIGFNAEAYNSNVPLIPKGSDGMSKRSIKKWKDKVENK

来源 Source

来源生物 organism	Bacillus amyloliquefaciens
NCBI Class编号 ncbi_taxonomy_id	1390
宿主生物 host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	352

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3bama_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.1 — Restriction endonuclease-like
Family Family family	c.52.1.3 — Restriction endonuclease BamHI

Domain ID domain_id	d3bamb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.1 — Restriction endonuclease-like
Family Family family	c.52.1.3 — Restriction endonuclease BamHI

CATH v4.4 (2 domains)

Domain ID domain_id	3bamA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	91 — Restriction Endonuclease
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3bamB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	91 — Restriction Endonuclease
Homologous superfamily homologous superfamily	20 —

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8. Citations (2)

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Unit-cell length a length_a	106.400 Å
Unit-cell length b length_b	79.600 Å
Unit-cell length c length_c	67.600 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2260
R_work r_work	0.2260
R_free r_free	0.2680

fit	/app/data/saxs_computation/ba/3bam/3bam.fit
pddf	/app/data/pr_computation/ba/3bam/3bam.pr.out
profile	/app/data/saxs_computation/ba/3bam/3bam.dat

RESTRICTION ENDONUCLEASE BAMHI COMPLEX WITH DNA AND MANGANESE IONS (POST-REACTIVE COMPLEX)

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

PROTEIN (RESTRICTION ENDONUCLEASE BAMHI)

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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

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)