SAXSdb — 3vhr

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

Capsular polysaccharide synthesis enzyme Cap5F

Staphylococcus aureus

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 FORMIC ACID × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q99X63_STAAM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–369； UniProt 1–369

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	3vhr
Deposition date deposition_date	2011-09-01
Structure title title	Crystal Structure of capsular polysaccharide assembling protein CapF from Staphylococcus aureus in space group C2221
Keywords keywords	Rossmann fold, Cupin DOmain, Short-chain dehydrogenase/reductase, NADPH-dependent UDP-4-hexulose reductase, Zn2+, OXIDOREDUCTASE; OXIDOREDUCTASE
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.

3vhr__assembly_1__model_1

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

Download this curve (.dat)

3vhr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3vhr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.99 Å
Rg (electron density)	32.96 Å
Total Rg	33.23 Å
Atom count	5566
Residues	676
Excluded volume	99451 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3vhr__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	Capsular polysaccharide synthesis enzyme Cap5F
Molecular weight formula_weight	42565.1 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	2811

MNIVITGAKGFVGKNLKADLTSTTDHHIFEVHRQTKEEELESALLKADFIVHLAGVNRPEHDKEFSLGNVSYLDHVLDILTRNTKKPAILLSSSIQATQDNPYGESKLQGEQLLREYAEEYGNTVYIYRWPNLFGKWCKPNYNSVIATFCYKIARNEEIQVNDRNVELTLNYVDDIVAEIKRAIEGTPTIENGVPTVPNVFKVTLGEIVDLLYKFKQSRLDRTLPKLDNLFEKDLYSTYLSYLPSTDFSYPLLMNVDDRGSFTEFIKTPDRGQVSVNISKPGITKGNHWHHTKNEKFLVVSGKGVIRFRHVNDDEIIEYYVSGDKLEVVDIPVGYTHNIENLGDTDMVTIMWVNEMFDPNQPDTYFLEV

Source Source

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	158878
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	FORMIC ACID
Molecular weight formula_weight	46.0 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	28

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3vhrA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	3vhrA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	10 — Jelly Rolls

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Unit-cell length a length_a	66.060 Å
Unit-cell length b length_b	105.010 Å
Unit-cell length c length_c	131.530 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	2.700 Å
Low-resolution limit resolution_low	48.470 Å
R factor r_factor	0.2013
R_work r_work	0.1984
R_free r_free	0.2592

Crystal Structure of capsular polysaccharide assembling protein CapF from Staphylococcus aureus in space group C2221

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

Capsular polysaccharide synthesis enzyme Cap5F

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

3vhr__assembly_1__model_1

3vhr__assembly_1__model_1 | I(q)

3vhr__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (2)

Crystal Structure of capsular polysaccharide assembling protein CapF from Staphylococcus aureus in space group C2221

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

Capsular polysaccharide synthesis enzyme Cap5F

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

3vhr__assembly_1__model_1

3vhr__assembly_1__model_1 | I(q)

3vhr__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) 2 domains

CATH v4.4 (2 domains)

7. Citations (2)