SAXSdb — 6o4a

▼

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

Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase

Burkholderia pseudomallei (strain 1710b)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	CALCIUM ION × 1 2-(pyridin-3-ylcarbonylamino)ethyl (2~{S})-1-(phenylmethyl)sulfonylpiperidine-2-carboxylate × 1 water × 1	Consistent with protein count
2	Insufficient information	Monomer	Protein 1	2-(pyridin-3-ylcarbonylamino)ethyl (2~{S})-1-(phenylmethyl)sulfonylpiperidine-2-carboxylate × 1 water × 1	Consistent with protein count
3	Insufficient information	Monomer	Protein 1	CALCIUM ION × 1 2-(pyridin-3-ylcarbonylamino)ethyl (2~{S})-1-(phenylmethyl)sulfonylpiperidine-2-carboxylate × 1 water × 1	Consistent with protein count
4	Insufficient information	Monomer	Protein 1	2-(pyridin-3-ylcarbonylamino)ethyl (2~{S})-1-(phenylmethyl)sulfonylpiperidine-2-carboxylate × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SMT3_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 11–96； UniProt 13–98 Author chain B； PDBConstruct 11–96； UniProt 13–98 Author chain C； PDBConstruct 11–96； UniProt 13–98 Author chain D； PDBConstruct 11–96； UniProt 13–98

Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase

Burkholderia pseudomallei (strain 1710b)

UniProt Q3JK38

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	CALCIUM ION × 1 2-(pyridin-3-ylcarbonylamino)ethyl (2~{S})-1-(phenylmethyl)sulfonylpiperidine-2-carboxylate × 1 water × 1	Consistent with protein count
2	Insufficient information	Monomer	Protein 1	2-(pyridin-3-ylcarbonylamino)ethyl (2~{S})-1-(phenylmethyl)sulfonylpiperidine-2-carboxylate × 1 water × 1	Consistent with protein count
3	Insufficient information	Monomer	Protein 1	CALCIUM ION × 1 2-(pyridin-3-ylcarbonylamino)ethyl (2~{S})-1-(phenylmethyl)sulfonylpiperidine-2-carboxylate × 1 water × 1	Consistent with protein count
4	Insufficient information	Monomer	Protein 1	2-(pyridin-3-ylcarbonylamino)ethyl (2~{S})-1-(phenylmethyl)sulfonylpiperidine-2-carboxylate × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q3JK38_BURP1
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 98–209； UniProt 2–113 Author chain B； PDBConstruct 98–209； UniProt 2–113 Author chain C； PDBConstruct 98–209； UniProt 2–113 Author chain D； PDBConstruct 98–209； UniProt 2–113

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6o4a
Deposition date deposition_date	2019-02-28
Structure title title	CRYSTAL STRUCTURE OF SMT FUSION PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FROM BURKHOLDERIA PSEUDOMALLEI COMPLEXED WITH SF355
Keywords keywords	;SSGCID, PEPTIDYL, PROLINE, ISOMERASE, SF355, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, PROTEIN BINDING ;; ISOMERASE, PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

▼

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.

6o4a__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6o4a__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6o4a__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	19.86 Å
Rg (electron density)	19.07 Å
Total Rg	19.95 Å
Atom count	1450
Residues	191
Excluded volume	25595 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6o4a__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6o4a__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6o4a__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6o4a__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase
Molecular weight formula_weight	23001.8 kDa
EC 编号 ec_number	5.2.1.8
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	6274

MGHHHHHHSGEVKPEVKPETHINLKVSDGSSEIFFKIKKTTPLRRLMEAFAKRQGKEMDSLRFLYDGIRIQADQTPEDLDMEDNDIIEAHREQIGGSTVVTTESGLKYEDLTEGSGAEARAGQTVSVHYTGWLTDGQKFDSSKDRNDPFAFVLGGGMVIKGWDEGVQGMKVGGVRRLTIPPQLGYGARGAGGVIPPNATLVFEVELLDV

Source Source

Source organism organism	Burkholderia pseudomallei (strain 1710b)
NCBI taxonomy ID ncbi_taxonomy_id	320372
Host organism host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	2-(pyridin-3-ylcarbonylamino)ethyl (2~{S})-1-(phenylmethyl)sulfonylpiperidine-2-carboxylate
Molecular weight formula_weight	431.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	502

▼

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6o4aA02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	50 — Chitinase A; domain 3
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	6o4aC02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	50 — Chitinase A; domain 3
Homologous superfamily homologous superfamily	40 —

▶

Unit-cell length a length_a	62.820 Å
Unit-cell length b length_b	32.650 Å
Unit-cell length c length_c	178.190 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.01 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	44.550 Å
R factor r_factor	0.1590
R_work r_work	0.1570
R_free r_free	0.2080

CRYSTAL STRUCTURE OF SMT FUSION PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FROM BURKHOLDERIA PSEUDOMALLEI COMPLEXED WITH SF355

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

Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase

State in the Current Structure

Other States of the Same Protein in the Database

Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase

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

6o4a__assembly_4__model_1

6o4a__assembly_4__model_1 | I(q)

6o4a__assembly_4__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 (1)

CRYSTAL STRUCTURE OF SMT FUSION PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FROM BURKHOLDERIA PSEUDOMALLEI COMPLEXED WITH SF355

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

Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ubiquitin-like protein SMT3,Peptidyl-prolyl cis-trans isomerase

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

6o4a__assembly_4__model_1

6o4a__assembly_4__model_1 | I(q)

6o4a__assembly_4__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 (1)