5opx

Crystal structure of the GroEL mutant A109C in complex with GroES and ADP BeF2

Method: X-RAY DIFFRACTION

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

60 kDa chaperonin

Escherichia coli (strain K12)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 28	10 kDa chaperonin × 14 （P0A6F9） ADENOSINE-5'-DIPHOSPHATE × 14 MAGNESIUM ION × 14 BERYLLIUM TRIFLUORIDE ION × 14 POTASSIUM ION × 14	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CH60_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–548； UniProt 1–548 Author chain B； PDBConstruct 1–548； UniProt 1–548 Author chain C； PDBConstruct 1–548； UniProt 1–548 Author chain D； PDBConstruct 1–548； UniProt 1–548 Author chain E； PDBConstruct 1–548； UniProt 1–548 Author chain F； PDBConstruct 1–548； UniProt 1–548 Author chain G； PDBConstruct 1–548； UniProt 1–548 Author chain H； PDBConstruct 1–548； UniProt 1–548 Author chain I； PDBConstruct 1–548； UniProt 1–548 Author chain J； PDBConstruct 1–548； UniProt 1–548 Author chain K； PDBConstruct 1–548； UniProt 1–548 Author chain L； PDBConstruct 1–548； UniProt 1–548 Author chain M； PDBConstruct 1–548； UniProt 1–548 Author chain N； PDBConstruct 1–548； UniProt 1–548

10 kDa chaperonin

Escherichia coli (strain K12)

UniProt P0A6F9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 28	60 kDa chaperonin × 14 （P0A6F5） ADENOSINE-5'-DIPHOSPHATE × 14 MAGNESIUM ION × 14 BERYLLIUM TRIFLUORIDE ION × 14 POTASSIUM ION × 14	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CH10_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain 1； PDBConstruct 1–97； UniProt 1–97 Author chain 2； PDBConstruct 1–97； UniProt 1–97 Author chain O； PDBConstruct 1–97； UniProt 1–97 Author chain P； PDBConstruct 1–97； UniProt 1–97 Author chain Q； PDBConstruct 1–97； UniProt 1–97 Author chain R； PDBConstruct 1–97； UniProt 1–97 Author chain S； PDBConstruct 1–97； UniProt 1–97 Author chain T； PDBConstruct 1–97； UniProt 1–97 Author chain U； PDBConstruct 1–97； UniProt 1–97 Author chain V； PDBConstruct 1–97； UniProt 1–97 Author chain W； PDBConstruct 1–97； UniProt 1–97 Author chain X； PDBConstruct 1–97； UniProt 1–97 Author chain Y； PDBConstruct 1–97； UniProt 1–97 Author chain Z； PDBConstruct 1–97； UniProt 1–97

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	5opx
Deposition date deposition_date	2017-08-10
Structure title title	Crystal structure of the GroEL mutant A109C in complex with GroES and ADP BeF2
Keywords keywords	chaperonin, CHAPERONE; CHAPERONE
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.

5opx__assembly_1__model_1

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

Download this curve (.dat)

5opx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5opx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	72.58 Å
Rg (electron density)	72.85 Å
Total Rg	72.76 Å
Atom count	63865
Residues	8571
Excluded volume	1143900 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5opx__assembly_1__model_1`	28-meric （28）	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 (6)

Entity 1 Entity 1 polymer

Description description	60 kDa chaperonin
Molecular weight formula_weight	57423.8 kDa
Mutation mutation	A109C
Source method src_method	man
Copy count entity_count	14

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N
Atom count atom_count	63865

MAAKDVKFGNDARVKMLRGVNVLADAVKVTLGPKGRNVVLDKSFGAPTITKDGVSVAREIELEDKFENMGAQMVKEVASKANDAAGDGTTTATVLAQAIITEGLKAVACGMNPMDLKRGIDKAVTAAVEELKALSVPCSDSKAIAQVGTISANSDETVGKLIAEAMDKVGKEGVITVEDGTGLQDELDVVEGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVAKAGKPLLIIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGVGEEAAIQGRVAQIRQQIEEATSDYDREKLQERVAKLAGGVAVIKVGAATEVEMKEKKARVEDALHATRAAVEEGVVAGGGVALIRVASKLADLRGQNEDQNVGIKVALRAMEAPLRQIVLNCGEEPSVVANTVKGGDGNYGYNAATEEYGNMIDMGILDPTKVTRSALQYAASVAGLMITTECMVTDLPKNDAADLGAAGGMGGMGGMGGMM

Source Source

Source organism organism	Escherichia coli (strain K12)
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	10 kDa chaperonin
Molecular weight formula_weight	10400.9 kDa
Source method src_method	man
Copy count entity_count	14

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1,2,O,P,Q,R,S,T,U,V,W,X,Y,Z

MNIRPLHDRVIVKRKEVETKSAGGIVLTGSAAAKSTRGEVLAVGNGRILENGEVKPLDVKVGDIVIFNDGYGVKSEKIDNEEVLIMSESDILAIVEA

Source Source

Source organism organism	Escherichia coli (strain K12)
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 5 Entity 5 non-polymer

Description description	BERYLLIUM TRIFLUORIDE ION
Molecular weight formula_weight	66.0 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 6 Entity 6 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	14

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6. Fold Classification (SCOP + CATH) 42 domains

CATH v4.4 (42 domains)

Domain ID domain_id	5opx100
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	33 — 10 Kd Chaperonin, Protein Cpn10; Chain O
Homologous superfamily homologous superfamily	40 — GroES chaperonin

Domain ID domain_id	5opx200
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	33 — 10 Kd Chaperonin, Protein Cpn10; Chain O
Homologous superfamily homologous superfamily	40 — GroES chaperonin

Domain ID domain_id	5opxA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	560 — GROEL; domain 1
Homologous superfamily homologous superfamily	10 — GroEL-like equatorial domain

Domain ID domain_id	5opxA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	260 — GROEL; domain 2
Homologous superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

Domain ID domain_id	5opxB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	560 — GROEL; domain 1
Homologous superfamily homologous superfamily	10 — GroEL-like equatorial domain

Domain ID domain_id	5opxB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	260 — GROEL; domain 2
Homologous superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

Domain ID domain_id	5opxC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	560 — GROEL; domain 1
Homologous superfamily homologous superfamily	10 — GroEL-like equatorial domain

Domain ID domain_id	5opxC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	260 — GROEL; domain 2
Homologous superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

Domain ID domain_id	5opxD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	560 — GROEL; domain 1
Homologous superfamily homologous superfamily	10 — GroEL-like equatorial domain

Domain ID domain_id	5opxD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	260 — GROEL; domain 2
Homologous superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

Domain ID domain_id	5opxE01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	560 — GROEL; domain 1
Homologous superfamily homologous superfamily	10 — GroEL-like equatorial domain

Domain ID domain_id	5opxE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	260 — GROEL; domain 2
Homologous superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

Domain ID domain_id	5opxF01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	560 — GROEL; domain 1
Homologous superfamily homologous superfamily	10 — GroEL-like equatorial domain

Domain ID domain_id	5opxF02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	260 — GROEL; domain 2
Homologous superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

Domain ID domain_id	5opxG01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	560 — GROEL; domain 1
Homologous superfamily homologous superfamily	10 — GroEL-like equatorial domain

Domain ID domain_id	5opxG02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	260 — GROEL; domain 2
Homologous superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

Domain ID domain_id	5opxH01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	560 — GROEL; domain 1
Homologous superfamily homologous superfamily	10 — GroEL-like equatorial domain

Domain ID domain_id	5opxH02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	260 — GROEL; domain 2
Homologous superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

Domain ID domain_id	5opxI01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	560 — GROEL; domain 1
Homologous superfamily homologous superfamily	10 — GroEL-like equatorial domain

Domain ID domain_id	5opxI02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	260 — GROEL; domain 2
Homologous superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

Domain ID domain_id	5opxJ01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	560 — GROEL; domain 1
Homologous superfamily homologous superfamily	10 — GroEL-like equatorial domain

Domain ID domain_id	5opxJ02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	260 — GROEL; domain 2
Homologous superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

Domain ID domain_id	5opxK01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	560 — GROEL; domain 1
Homologous superfamily homologous superfamily	10 — GroEL-like equatorial domain

Domain ID domain_id	5opxK02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	260 — GROEL; domain 2
Homologous superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

Domain ID domain_id	5opxL01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	560 — GROEL; domain 1
Homologous superfamily homologous superfamily	10 — GroEL-like equatorial domain

Domain ID domain_id	5opxL02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	260 — GROEL; domain 2
Homologous superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

Domain ID domain_id	5opxM01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	560 — GROEL; domain 1
Homologous superfamily homologous superfamily	10 — GroEL-like equatorial domain

Domain ID domain_id	5opxM02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	260 — GROEL; domain 2
Homologous superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

Domain ID domain_id	5opxN01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	560 — GROEL; domain 1
Homologous superfamily homologous superfamily	10 — GroEL-like equatorial domain

Domain ID domain_id	5opxN02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	260 — GROEL; domain 2
Homologous superfamily homologous superfamily	10 — TCP-1-like chaperonin intermediate domain

Domain ID domain_id	5opxO00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	33 — 10 Kd Chaperonin, Protein Cpn10; Chain O
Homologous superfamily homologous superfamily	40 — GroES chaperonin

Domain ID domain_id	5opxP00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	33 — 10 Kd Chaperonin, Protein Cpn10; Chain O
Homologous superfamily homologous superfamily	40 — GroES chaperonin

Domain ID domain_id	5opxQ00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	33 — 10 Kd Chaperonin, Protein Cpn10; Chain O
Homologous superfamily homologous superfamily	40 — GroES chaperonin

Domain ID domain_id	5opxR00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	33 — 10 Kd Chaperonin, Protein Cpn10; Chain O
Homologous superfamily homologous superfamily	40 — GroES chaperonin

Domain ID domain_id	5opxS00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	33 — 10 Kd Chaperonin, Protein Cpn10; Chain O
Homologous superfamily homologous superfamily	40 — GroES chaperonin

Domain ID domain_id	5opxT00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	33 — 10 Kd Chaperonin, Protein Cpn10; Chain O
Homologous superfamily homologous superfamily	40 — GroES chaperonin

Domain ID domain_id	5opxU00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	33 — 10 Kd Chaperonin, Protein Cpn10; Chain O
Homologous superfamily homologous superfamily	40 — GroES chaperonin

Domain ID domain_id	5opxV00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	33 — 10 Kd Chaperonin, Protein Cpn10; Chain O
Homologous superfamily homologous superfamily	40 — GroES chaperonin

Domain ID domain_id	5opxW00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	33 — 10 Kd Chaperonin, Protein Cpn10; Chain O
Homologous superfamily homologous superfamily	40 — GroES chaperonin

Domain ID domain_id	5opxX00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	33 — 10 Kd Chaperonin, Protein Cpn10; Chain O
Homologous superfamily homologous superfamily	40 — GroES chaperonin

Domain ID domain_id	5opxY00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	33 — 10 Kd Chaperonin, Protein Cpn10; Chain O
Homologous superfamily homologous superfamily	40 — GroES chaperonin

Domain ID domain_id	5opxZ00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	33 — 10 Kd Chaperonin, Protein Cpn10; Chain O
Homologous superfamily homologous superfamily	40 — GroES chaperonin

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Unit-cell length a length_a	217.567 Å
Unit-cell length b length_b	230.504 Å
Unit-cell length c length_c	235.391 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	56

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

Resolution resolution	3.640 Å
Low-resolution limit resolution_low	50.010 Å
R factor r_factor	0.2324
R_work r_work	0.2312
R_free r_free	0.2560

Crystal structure of the GroEL mutant A109C in complex with GroES and ADP BeF2

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

60 kDa chaperonin

State in the Current Structure

Other States of the Same Protein in the Database

10 kDa chaperonin

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

5opx__assembly_1__model_1

5opx__assembly_1__model_1 | I(q)

5opx__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 (6)

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

6. Fold Classification (SCOP + CATH) 42 domains

CATH v4.4 (42 domains)

7. Citations (1)

Crystal structure of the GroEL mutant A109C in complex with GroES and ADP BeF2

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

60 kDa chaperonin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

10 kDa chaperonin

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

5opx__assembly_1__model_1

5opx__assembly_1__model_1 | I(q)

5opx__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 (6)

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

6. Fold Classification (SCOP + CATH) 42 domains

CATH v4.4 (42 domains)

7. Citations (1)