SAXSdb — 3dev

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

SH1221

Staphylococcus haemolyticus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 3 MAGNESIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q4L745_STAHJ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–312； UniProt 1–312 Author chain B； PDBConstruct 1–312； UniProt 1–312

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	3dev
Deposition date deposition_date	2008-06-10
Structure title title	Crystal structure of SH1221 protein from Staphylococcus haemolyticus, Northeast Structural Genomics Consortium Target ShR87
Keywords keywords	;alpha-beta protein., Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, unknown function ;; structural genomics, unknown function
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.

3dev__assembly_1__model_1

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

Download this curve (.dat)

3dev__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dev__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.39 Å
Rg (electron density)	27.46 Å
Total Rg	28.11 Å
Atom count	5053
Residues	620
Excluded volume	89112 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dev__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 (4)

Entity 1 Entity 1 polymer

Description description	SH1221
Molecular weight formula_weight	36589.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5089

MVEIFNEIMQRVKEAETIIIHRHVRPDPDAYGSQLGLKLYLERKFPEKNIYATGEAEPSLSFIGDLDEIDDSVYSDALVIVCDTANAPRIDDQRYLNGQSLIKIDHHPATDQYGDVNFVNTEASSTSEIIFDFISHFNDLSIIDEHVARVLYLGIVGDTGRFLFSNTSPHTMEVASQLLAYPFNHNAELNKMSEKDPKLMPFQGYVLQNFELSDSHEYCQIKITNDVLKQFDIQPNEASQFVNTVADISGLKIWMFGVDEGDQIRCRIRSKGITINDVANQFGGGGHPNASGVSVYSWDEFEELAQALRQKLLEHHHHHH

Source Source

Source organism organism	Staphylococcus haemolyticus
NCBI taxonomy ID ncbi_taxonomy_id	279808
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	36

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3devA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1640 — inorganic pyrophosphatase (n-terminal core)
Homologous superfamily homologous superfamily	10 — inorganic pyrophosphatase (n-terminal core)

Domain ID domain_id	3devA02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	3devB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1640 — inorganic pyrophosphatase (n-terminal core)
Homologous superfamily homologous superfamily	10 — inorganic pyrophosphatase (n-terminal core)

Domain ID domain_id	3devB02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	310 — Diaminopimelate Epimerase; Chain A, domain 1
Homologous superfamily homologous superfamily	30 —

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Unit-cell length a length_a	106.087 Å
Unit-cell length b length_b	106.087 Å
Unit-cell length c length_c	86.092 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 3
Space-group number int_tables_number	143
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	19.940 Å
R factor r_factor	0.1930
R_work r_work	0.1930
R_free r_free	0.2450

Crystal structure of SH1221 protein from Staphylococcus haemolyticus, Northeast Structural Genomics Consortium Target ShR87

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

SH1221

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

3dev__assembly_1__model_1

3dev__assembly_1__model_1 | I(q)

3dev__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of SH1221 protein from Staphylococcus haemolyticus, Northeast Structural Genomics Consortium Target ShR87

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

SH1221

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

3dev__assembly_1__model_1

3dev__assembly_1__model_1 | I(q)

3dev__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)