SAXSdb — 3csv

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

Aminoglycoside phosphotransferase

Silicibacter sp.

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 SODIUM ION × 2 CHLORIDE ION × 2 SULFATE ION × 2 1,2-ETHANEDIOL × 22 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q1GCP1_SILST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–333； UniProt 1–332

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	3csv
Deposition date deposition_date	2008-04-10
Structure title title	Crystal structure of a putative aminoglycoside phosphotransferase (YP_614837.1) from Silicibacter sp. TM1040 at 2.15 A resolution
Keywords keywords	;YP_614837.1, Putative Aminoglycoside Phosphotransferase, Phosphotransferase enzyme family, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, TRANSFERASE ;; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3csv__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3csv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3csv__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	31.89 Å
Rg (electron density)	31.74 Å
Total Rg	32.08 Å
Atom count	5166
Residues	632
Excluded volume	91545 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3csv__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Aminoglycoside phosphotransferase
Molecular weight formula_weight	38195.9 kDa
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	2807

GMTSREDEIRDFLATHGYADWNRTPLAGDASSRRYQRLRSPTGAKAVLMDWSPEEGGDTQPFVDLAQYLRNLDISAPEIYAEEHARGLLLIEDLGDALFTEVINNDPAQEMPLYRAAVDLLIHLHDAQTPELARLDPETLSEMTRLAFSEYRYAILGDAAEDNRKRFEHRFAQILSAQLEGDMVFVHRDFHAQNLLWLPEREGLARVGVIDFQDAKLGHRAYDLVSLLQDARRDVPAQVEAQMIDHYIQATGVDESHFRSAYAVIAVQRNMRILGIFARLSQRFGKRHYIEFVPRVWAHFERGLAHPALASAAEEILNALPAPAPEVLERLRA

Source Source

Source organism organism	Silicibacter sp.
NCBI taxonomy ID ncbi_taxonomy_id	292414
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	199

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3csvA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	3csvA02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1200 — Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Aminoglycoside phosphotransferase (APH), C-terminal lobe

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Unit-cell length a length_a	113.680 Å
Unit-cell length b length_b	55.940 Å
Unit-cell length c length_c	61.220 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.90 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	29.735 Å
R factor r_factor	0.1710
R_work r_work	0.1680
R_free r_free	0.2280

Crystal structure of a putative aminoglycoside phosphotransferase (YP_614837.1) from Silicibacter sp. TM1040 at 2.15 A resolution

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

Aminoglycoside phosphotransferase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3csv__assembly_1__model_1

3csv__assembly_1__model_1 | I(q)

3csv__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of a putative aminoglycoside phosphotransferase (YP_614837.1) from Silicibacter sp. TM1040 at 2.15 A resolution

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

Aminoglycoside phosphotransferase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3csv__assembly_1__model_1

3csv__assembly_1__model_1 | I(q)

3csv__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)