SAXSdb — 3zvr

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

DYNAMIN-1

RATTUS NORVEGICUS

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–752	Fragment：DYNAMIN 1 G397D DELTA PRD, RESIDUES 1-752 Mutation：YES	1PE PENTAETHYLENE GLYCOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.7；52.5 MM TRIS.HCL PH 7.7, 175 MM NACL, 32.5 MM NANO3, 20 % V/V PEG 400, 0.97 MM BETA-MERCAPTOETHANOL, 31.9 MICROM DYN1 G397D DELTA PRD	Resolution 3.10 Å R-free 0.272

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 3ZVR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2AKA Structure of the nucleotide-free myosin II motor domain from Dictyostelium discoideum fused to the GTPase domain of dynamin 1 from Rattus norvegicus Deposited 2005-08-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 6–304（299 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；Tris, PEG 8000, MPD, DTT, magnesium chloride, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.224

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DYN1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–772； UniProt 1–752

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	3zvr
Deposition date deposition_date	2011-07-27
Structure title title	Crystal structure of Dynamin
Keywords keywords	HYDROLASE, DRP1, DRP, ENDOCYTOSIS, MITOCHONDRIAL FISSION, GTPASE, STALK, PH, BSE, MEMBRANE FISSION; HYDROLASE
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	51.66 Å
Radius of gyration Rg (electron density) rg_electron	52.89 Å
Forward intensity I(0) i0	87470100.00
Molecular weight molecular_weight	77672.0 kDa
Excluded volume excluded_volume	97689 Å³
Envelope volume envelope_volume	164070 Å³
Hydration-shell volume shell_volume	28334 Å³
Envelope diameter envelope_diameter	171.4 Å
Shell Rg shell_rg	49.93 Å
Envelope Rg envelope_rg	51.58 Å
Shape Rg shape_rg	52.99 Å
Total Rg total_rg	52.42 Å
Total atoms total_atoms	10945
Residues n_residues	669
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	161.0 Å
Rg (real space) rg_real	52.38 Å
Rg uncertainty (real space) rg_real_error	2.09 Å
I(0) (real space) i0_real	8.7470e+07
I(0) uncertainty (real space) i0_real_error	1.8620e+06
Rg (reciprocal space) rg_reciprocal	51.03 Å
I(0) (reciprocal space) i0_reciprocal	87310000.0000
Solution quality estimate total_estimate	0.6118
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.8 Å
Skewness Skewness skewness	0.456
Kurtosis Kurtosis kurtosis	-0.868
Angular range angular_range	— – 0.1500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2302000.0000
Real-space data points n_real_points	31
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.273; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.130; 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	DYNAMIN-1
Molecular weight formula_weight	88362.6 kDa
EC 编号 ec_number	3.6.5.5
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	10950

MGSSHHHHHHSSGLVPRGSHMGNRGMEDLIPLVNRLQDAFSAIGQNADLDLPQIAVVGGQSAGKSSVLENFVGRDFLPRGSGIVTRRPLVLQLVNSTTEYAEFLHCKGKKFTDFEEVRLEIEAETDRVTGTNKGISPVPINLRVYSPHVLNLTLVDLPGMTKVPVGDQPPDIEFQIRDMLMQFVTKENCLILAVSPANSDLANSDALKIAKEVDPQGQRTIGVITKLDLMDEGTDARDVLENKLLPLRRGYIGVVNRSQKDIDGKKDITAALAAERKFFLSHPSYRHLADRMGTPYLQKVLNQQLTNHIRDTLPGLRNKLQSQLLSIEKEVDEYKNFRPDDPARKTKALLQMVQQFAVDFEKRIEGSGDQIDTYELSGGARINRIFHERFPFELVKMEFDEKELRREISYAIKNIHDIRTGLFTPDLAFEATVKKQVQKLKEPSIKCVDMVVSELTSTIRKCSEKLQQYPRLREEMERIVTTHIREREGRTKEQVMLLIDIELAYMNTNHEDFIGFANAQQRSNQMNKKKTSGNQDEILVIRKGWLTINNIGIMKGGSKEYWFVLTAENLSWYKDDEEKEKKYMLSVDNLKLRDVEKGFMSSKHIFALFNTEQRNVYKDYRQLELACETQEEVDSWKASFLRAGVYPERVGDKEKASETEENGSDSFMHSMDPQLERQVETIRNLVDSYMAIVNKTVRDLMPKTIMHLMINNTKEFIFSELLANLYSCGDQNTLMEESAEQAQRRDEMLRMYHALKEALSIIGDINTTTVST

来源 Source

来源生物 organism	RATTUS NORVEGICUS
通用名 common_name	NORWAY RAT
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	5

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	3zvrA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	3zvrA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1240 — Dynamin, middle domain

Domain ID domain_id	3zvrA03
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

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8. Citations (1)

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Unit-cell length a length_a	178.450 Å
Unit-cell length b length_b	191.610 Å
Unit-cell length c length_c	60.520 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	95.805 Å
R factor r_factor	0.2153
R_work r_work	0.2123
R_free r_free	0.2720

fit	/app/data/saxs_computation/zv/3zvr/3zvr.fit
pddf	/app/data/pr_computation/zv/3zvr/3zvr.pr.out
profile	/app/data/saxs_computation/zv/3zvr/3zvr.dat

Crystal structure of Dynamin

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

DYNAMIN-1

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