SAXSdb — 1d02

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

TYPE II RESTRICTION ENZYME MUNI

Mycoplasma

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 1–202 Chain B； UniProt 1–202	Mutation：D83A	;DNA (5'-D(GPCPCPAPAPTPTPGPGPC)-3') ; × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；PEG 8000, CALCIUM CHLORIDE, SODIUM CHLORIDE, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K	Resolution 1.70 Å R-free 0.213

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	T2MU_MYCSP
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–202； UniProt 1–202 Author chain B； PDBConstruct 1–202； UniProt 1–202

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	1d02
Deposition date deposition_date	1999-09-08
Structure title title	CRYSTAL STRUCTURE OF MUNI RESTRICTION ENDONUCLEASE IN COMPLEX WITH COGNATE DNA
Keywords keywords	ALPHA/BETA PROTEIN, PROTEIN-DNA COMPLEX, DISTORTED DOUBLE HELIX, 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	23.53 Å
Radius of gyration Rg (electron density) rg_electron	22.68 Å
Forward intensity I(0) i0	49450700.00
Molecular weight molecular_weight	52038.0 kDa
Excluded volume excluded_volume	63906 Å³
Envelope volume envelope_volume	74572 Å³
Hydration-shell volume shell_volume	27212 Å³
Envelope diameter envelope_diameter	83.2 Å
Shell Rg shell_rg	30.10 Å
Envelope Rg envelope_rg	23.00 Å
Shape Rg shape_rg	22.66 Å
Total Rg total_rg	23.56 Å
Total atoms total_atoms	3666
Residues n_residues	417
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	79.7 Å
Rg (real space) rg_real	23.48 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	4.9450e+07
I(0) uncertainty (real space) i0_real_error	6.7330e+05
Rg (reciprocal space) rg_reciprocal	23.49 Å
I(0) (reciprocal space) i0_reciprocal	49450000.0000
Solution quality estimate total_estimate	0.7895
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	29.9 Å
Skewness Skewness skewness	0.350
Kurtosis Kurtosis kurtosis	-0.072
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11550000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.756; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; 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)

Entity 1 Entity 1 polymer

Description description	;DNA (5'-D(GPCPCPAPAPTPTPGPGPC)-3') ;
Molecular weight formula_weight	3045.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,D
Atom count atom_count	4312

GCCAATTGGC

Entity 2 Entity 2 polymer

Description description	TYPE II RESTRICTION ENZYME MUNI
Molecular weight formula_weight	23376.5 kDa
EC 编号 ec_number	3.1.21.4
Mutation mutation	D83A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MGKSELSGRLNWQALAGLKASGAEQNLYNVFNAVFEGTKYVLYEKPKHLKNLYAQVVLPDDVIKEIFNPLIDLSTTQWGVSPAFAIENTETHKILFGEIKRQDGWVEGKDPSAGRGNAHERSCKLFTPGLLKAYRTIGGINDEEILPFWVVFEGDITRDPKRVREITFWYDHYQDNYFMWRPNESGEKLVQHFNEKLKKYLD

来源 Source

来源生物 organism	Mycoplasma
NCBI Class编号 ncbi_taxonomy_id	2093
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	646

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1d02a_
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.52.1.8 — Restriction endonuclease MunI

Domain ID domain_id	d1d02b_
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.52.1.8 — Restriction endonuclease MunI

CATH v4.4 (2 domains)

Domain ID domain_id	1d02A00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	580 — ECO RI Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — Eco RI Endonuclease, subunit A

Domain ID domain_id	1d02B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	580 — ECO RI Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — Eco RI Endonuclease, subunit A

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8. Citations (1)

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Unit-cell length a length_a	58.400 Å
Unit-cell length b length_b	72.470 Å
Unit-cell length c length_c	121.670 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	1.700 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1800
R_work r_work	0.1800
R_free r_free	0.2130

fit	/app/data/saxs_computation/d0/1d02/1d02.fit
pddf	/app/data/pr_computation/d0/1d02/1d02.pr.out
profile	/app/data/saxs_computation/d0/1d02/1d02.dat

CRYSTAL STRUCTURE OF MUNI RESTRICTION ENDONUCLEASE IN COMPLEX WITH COGNATE DNA

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

TYPE II RESTRICTION ENZYME MUNI

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)