8vri

E. coli peptidyl-prolyl cis-trans isomerase containing difluoro-leucines

Method: X-RAY DIFFRACTION

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

Peptidyl-prolyl cis-trans isomerase B

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	DI(HYDROXYETHYL)ETHER × 1 TRIETHYLENE GLYCOL × 1 1,2-ETHANEDIOL × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	DI(HYDROXYETHYL)ETHER × 1 1,2-ETHANEDIOL × 3 TETRAETHYLENE GLYCOL × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	1,2-ETHANEDIOL × 1 NONAETHYLENE GLYCOL × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	1,2-ETHANEDIOL × 6 NONAETHYLENE GLYCOL × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PPIB_ECOLI
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–164； UniProt 1–164 Author chain B； PDBConstruct 1–164； UniProt 1–164 Author chain C； PDBConstruct 1–164； UniProt 1–164 Author chain D； PDBConstruct 1–164； UniProt 1–164 Author chain E； PDBConstruct 1–164； UniProt 1–164

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	8vri
Deposition date deposition_date	2024-01-22
Structure title title	E. coli peptidyl-prolyl cis-trans isomerase containing difluoro-leucines
Keywords keywords	Peptidyl-prolyl cis-trans isomerase, Non-canonical amino acids, fluorinated leucine, ISOMERASE; ISOMERASE
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.

8vri__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8vri__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8vri__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	17.06 Å
Rg (electron density)	15.70 Å
Total Rg	16.68 Å
Atom count	1380
Residues	164
Excluded volume	24221 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8vri__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8vri__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`8vri__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`8vri__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`8vri__assembly_5__model_1`	monomeric （1）	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 (8)

Entity 1 Entity 1 polymer

Description description	Peptidyl-prolyl cis-trans isomerase B
Molecular weight formula_weight	19211.2 kDa
EC 编号 ec_number	5.2.1.8
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	7798

MVTFHTNHGDIVIKTFDDKAPETVKNFXDYCREGFYNNTIFHRVINGFMIQGGGFEPGMKQKATKEPIKNEANNGXKNTRGTXAMARTQAPHSATAQFFINVVDNDFXNFSGESXQGWGYCVFAEVVDGMDVVDKIKGVATGRSGMHQDVPKEDVIIESVTVSEHHHHHH

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Peptidyl-prolyl cis-trans isomerase B
Molecular weight formula_weight	19183.2 kDa
EC 编号 ec_number	5.2.1.8
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,E

MVTFHTNHGDIVIKTFDDKAPETVKNFXDYCREGFYNNTIFHRVINGFMIQGGGFEPGMKQKATKEPIKNEANNGXKNTRGTXAMARTQAPHSATAQFFINVVDNDFXNFSGESXQGWGYCVFAEVVDGMDVVDKIKGVATGRSGMHQDVPKEDVIIESVTVSEHHHHHH

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 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 6 Entity 6 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	NONAETHYLENE GLYCOL
Molecular weight formula_weight	414.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	893

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Unit-cell length a length_a	78.655 Å
Unit-cell length b length_b	83.442 Å
Unit-cell length c length_c	122.141 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	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	24.120 Å
R factor r_factor	0.1850
R_work r_work	0.1828
R_free r_free	0.2242

E. coli peptidyl-prolyl cis-trans isomerase containing difluoro-leucines

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

Peptidyl-prolyl cis-trans isomerase B

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

8vri__assembly_2__model_1

8vri__assembly_2__model_1 | I(q)

8vri__assembly_2__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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 non-polymer

Entity 8 Entity 8 water

7. Citations (1)

E. coli peptidyl-prolyl cis-trans isomerase containing difluoro-leucines

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

Peptidyl-prolyl cis-trans isomerase B

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

8vri__assembly_2__model_1

8vri__assembly_2__model_1 | I(q)

8vri__assembly_2__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

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 non-polymer

Entity 8 Entity 8 water

7. Citations (1)