9WBT | pdb_00009wbt

Crystal Structure of Escherichia coli GroEL with Magnesium Ions and a Phosphorylated Serine Residue-3.2A

PDB DOI: https://doi.org/10.2210/pdb9WBT/pdb

Classification: CHAPERONE
Organism(s): Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-08-15 Released: 2025-09-03
Deposition Author(s): Guo, Y., Zhang, L., Zheng, H., Li, J., Han, Q.
Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.236 (Depositor), 0.232 (DCC)
R-Value Work:
0.196 (Depositor), 0.196 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of Escherichia coli GroEL with Magnesium Ions and a Phosphorylated Serine Residue

Guo, Y., Zhang, L., Zheng, H., Li, J., Han, Q.

To be published.

Macromolecule Content

Total Structure Weight: 810.16 kDa
Atom Count: 54,517
Modeled Residue Count: 7,348
Deposited Residue Count: 7,672
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chaperonin GroEL	A, B, E, F, H A, B, E, F, H, J, M	548	Escherichia coli BL21(DE3)	Mutation(s): 0 EC: 5.6.1.7
UniProt
Find proteins for P0A6F5 (Escherichia coli (strain K12)) Explore P0A6F5 Go to UniProtKB: P0A6F5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A6F5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Chaperonin GroEL	C, D, G, I, K C, D, G, I, K, L, N	548	Escherichia coli BL21(DE3)	Mutation(s): 0 EC: 5.6.1.7
UniProt
Find proteins for P0A6F5 (Escherichia coli (strain K12)) Explore P0A6F5 Go to UniProtKB: P0A6F5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0A6F5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TAM Query on TAM Download Ideal Coordinates CCD File SDF format, chain YA [auth G] SDF format, chain PB [auth J] SDF format, chain KB [auth I] MOL2 format, chain YA [auth G] MOL2 format, chain PB [auth J] MOL2 format, chain KB [auth I] mmCIF format, chain YA [auth G] mmCIF format, chain PB [auth J] mmCIF format, chain KB [auth I]	KB [auth I], PB [auth J], YA [auth G]	TRIS(HYDROXYETHYL)AMINOMETHANE C₇ H₁₇ N O₃ GKODZWOPPOTFGA-UHFFFAOYSA-N		Interactions Focus chain KB [auth I] Focus chain PB [auth J] Focus chain YA [auth G] Interactions & Density Focus chain KB [auth I] Focus chain PB [auth J] Focus chain YA [auth G]
HEZ Query on HEZ Download Ideal Coordinates CCD File SDF format, chain ZA [auth G] SDF format, chain YB [auth M] SDF format, chain WB [auth L] SDF format, chain W [auth B] SDF format, chain VA [auth F] SDF format, chain V [auth B] SDF format, chain UB [auth K] SDF format, chain UA [auth F] SDF format, chain QB [auth J] SDF format, chain P [auth A] SDF format, chain OA [auth E] SDF format, chain O [auth A] SDF format, chain NA [auth E] SDF format, chain MB [auth I] SDF format, chain MA [auth E] SDF format, chain LB [auth I] SDF format, chain IA [auth D] SDF format, chain HA [auth D] SDF format, chain GB [auth H] SDF format, chain FB [auth H] SDF format, chain CA [auth C] SDF format, chain BA [auth C] SDF format, chain AC [auth N] MOL2 format, chain ZA [auth G] MOL2 format, chain YB [auth M] MOL2 format, chain WB [auth L] MOL2 format, chain W [auth B] MOL2 format, chain VA [auth F] MOL2 format, chain V [auth B] MOL2 format, chain UB [auth K] MOL2 format, chain UA [auth F] MOL2 format, chain QB [auth J] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain MB [auth I] MOL2 format, chain MA [auth E] MOL2 format, chain LB [auth I] MOL2 format, chain IA [auth D] MOL2 format, chain HA [auth D] MOL2 format, chain GB [auth H] MOL2 format, chain FB [auth H] MOL2 format, chain CA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain AC [auth N] mmCIF format, chain ZA [auth G] mmCIF format, chain YB [auth M] mmCIF format, chain WB [auth L] mmCIF format, chain W [auth B] mmCIF format, chain VA [auth F] mmCIF format, chain V [auth B] mmCIF format, chain UB [auth K] mmCIF format, chain UA [auth F] mmCIF format, chain QB [auth J] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth E] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth E] mmCIF format, chain MB [auth I] mmCIF format, chain MA [auth E] mmCIF format, chain LB [auth I] mmCIF format, chain IA [auth D] mmCIF format, chain HA [auth D] mmCIF format, chain GB [auth H] mmCIF format, chain FB [auth H] mmCIF format, chain CA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain AC [auth N]	AC [auth N] BA [auth C] CA [auth C] FB [auth H] GB [auth H] AC [auth N], BA [auth C], CA [auth C], FB [auth H], GB [auth H], HA [auth D], IA [auth D], LB [auth I], MA [auth E], MB [auth I], NA [auth E], O [auth A], OA [auth E], P [auth A], QB [auth J], UA [auth F], UB [auth K], V [auth B], VA [auth F], W [auth B], WB [auth L], YB [auth M], ZA [auth G]	HEXANE-1,6-DIOL C₆ H₁₄ O₂ XXMIOPMDWAUFGU-UHFFFAOYSA-N		Interactions Focus chain AC [auth N] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain FB [auth H] Focus chain GB [auth H] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain LB [auth I] Focus chain MA [auth E] Focus chain MB [auth I] Focus chain NA [auth E] Focus chain O [auth A] Focus chain OA [auth E] Focus chain P [auth A] Focus chain QB [auth J] Focus chain UA [auth F] Focus chain UB [auth K] Focus chain V [auth B] Focus chain VA [auth F] Focus chain W [auth B] Focus chain WB [auth L] Focus chain YB [auth M] Focus chain ZA [auth G] Interactions & Density Focus chain AC [auth N] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain FB [auth H] Focus chain GB [auth H] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain LB [auth I] Focus chain MA [auth E] Focus chain MB [auth I] Focus chain NA [auth E] Focus chain O [auth A] Focus chain OA [auth E] Focus chain P [auth A] Focus chain QB [auth J] Focus chain UA [auth F] Focus chain UB [auth K] Focus chain V [auth B] Focus chain VA [auth F] Focus chain W [auth B] Focus chain WB [auth L] Focus chain YB [auth M] Focus chain ZA [auth G]
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain ZB [auth M] SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain XB [auth L] SDF format, chain XA [auth F] SDF format, chain X [auth B] SDF format, chain VB [auth K] SDF format, chain U [auth A] SDF format, chain TB [auth J] SDF format, chain TA [auth E] SDF format, chain T [auth A] SDF format, chain SB [auth J] SDF format, chain SA [auth E] SDF format, chain S [auth A] SDF format, chain RB [auth J] SDF format, chain RA [auth E] SDF format, chain R [auth A] SDF format, chain QA [auth E] SDF format, chain OB [auth I] SDF format, chain NB [auth I] SDF format, chain LA [auth D] SDF format, chain KA [auth D] SDF format, chain JB [auth H] SDF format, chain IB [auth H] SDF format, chain GA [auth C] SDF format, chain FA [auth C] SDF format, chain EB [auth G] SDF format, chain EA [auth C] SDF format, chain DC [auth N] SDF format, chain DB [auth G] SDF format, chain DA [auth C] SDF format, chain CC [auth N] SDF format, chain CB [auth G] SDF format, chain BB [auth G] SDF format, chain AA [auth B] MOL2 format, chain ZB [auth M] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain XB [auth L] MOL2 format, chain XA [auth F] MOL2 format, chain X [auth B] MOL2 format, chain VB [auth K] MOL2 format, chain U [auth A] MOL2 format, chain TB [auth J] MOL2 format, chain TA [auth E] MOL2 format, chain T [auth A] MOL2 format, chain SB [auth J] MOL2 format, chain SA [auth E] MOL2 format, chain S [auth A] MOL2 format, chain RB [auth J] MOL2 format, chain RA [auth E] MOL2 format, chain R [auth A] MOL2 format, chain QA [auth E] MOL2 format, chain OB [auth I] MOL2 format, chain NB [auth I] MOL2 format, chain LA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain JB [auth H] MOL2 format, chain IB [auth H] MOL2 format, chain GA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain EB [auth G] MOL2 format, chain EA [auth C] MOL2 format, chain DC [auth N] MOL2 format, chain DB [auth G] MOL2 format, chain DA [auth C] MOL2 format, chain CC [auth N] MOL2 format, chain CB [auth G] MOL2 format, chain BB [auth G] MOL2 format, chain AA [auth B] mmCIF format, chain ZB [auth M] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain XB [auth L] mmCIF format, chain XA [auth F] mmCIF format, chain X [auth B] mmCIF format, chain VB [auth K] mmCIF format, chain U [auth A] mmCIF format, chain TB [auth J] mmCIF format, chain TA [auth E] mmCIF format, chain T [auth A] mmCIF format, chain SB [auth J] mmCIF format, chain SA [auth E] mmCIF format, chain S [auth A] mmCIF format, chain RB [auth J] mmCIF format, chain RA [auth E] mmCIF format, chain R [auth A] mmCIF format, chain QA [auth E] mmCIF format, chain OB [auth I] mmCIF format, chain NB [auth I] mmCIF format, chain LA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain JB [auth H] mmCIF format, chain IB [auth H] mmCIF format, chain GA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain EB [auth G] mmCIF format, chain EA [auth C] mmCIF format, chain DC [auth N] mmCIF format, chain DB [auth G] mmCIF format, chain DA [auth C] mmCIF format, chain CC [auth N] mmCIF format, chain CB [auth G] mmCIF format, chain BB [auth G] mmCIF format, chain AA [auth B]	AA [auth B] BB [auth G] CB [auth G] CC [auth N] DA [auth C] AA [auth B], BB [auth G], CB [auth G], CC [auth N], DA [auth C], DB [auth G], DC [auth N], EA [auth C], EB [auth G], FA [auth C], GA [auth C], IB [auth H], JB [auth H], KA [auth D], LA [auth D], NB [auth I], OB [auth I], QA [auth E], R [auth A], RA [auth E], RB [auth J], S [auth A], SA [auth E], SB [auth J], T [auth A], TA [auth E], TB [auth J], U [auth A], VB [auth K], X [auth B], XA [auth F], XB [auth L], Y [auth B], Z [auth B], ZB [auth M]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BB [auth G] Focus chain CB [auth G] Focus chain CC [auth N] Focus chain DA [auth C] Focus chain DB [auth G] Focus chain DC [auth N] Focus chain EA [auth C] Focus chain EB [auth G] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain IB [auth H] Focus chain JB [auth H] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain NB [auth I] Focus chain OB [auth I] Focus chain QA [auth E] Focus chain R [auth A] Focus chain RA [auth E] Focus chain RB [auth J] Focus chain S [auth A] Focus chain SA [auth E] Focus chain SB [auth J] Focus chain T [auth A] Focus chain TA [auth E] Focus chain TB [auth J] Focus chain U [auth A] Focus chain VB [auth K] Focus chain X [auth B] Focus chain XA [auth F] Focus chain XB [auth L] Focus chain Y [auth B] Focus chain Z [auth B] Focus chain ZB [auth M] Interactions & Density Focus chain AA [auth B] Focus chain BB [auth G] Focus chain CB [auth G] Focus chain CC [auth N] Focus chain DA [auth C] Focus chain DB [auth G] Focus chain DC [auth N] Focus chain EA [auth C] Focus chain EB [auth G] Focus chain FA [auth C] Focus chain GA [auth C] Focus chain IB [auth H] Focus chain JB [auth H] Focus chain KA [auth D] Focus chain LA [auth D] Focus chain NB [auth I] Focus chain OB [auth I] Focus chain QA [auth E] Focus chain R [auth A] Focus chain RA [auth E] Focus chain RB [auth J] Focus chain S [auth A] Focus chain SA [auth E] Focus chain SB [auth J] Focus chain T [auth A] Focus chain TA [auth E] Focus chain TB [auth J] Focus chain U [auth A] Focus chain VB [auth K] Focus chain X [auth B] Focus chain XA [auth F] Focus chain XB [auth L] Focus chain Y [auth B] Focus chain Z [auth B] Focus chain ZB [auth M]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain AB [auth G] SDF format, chain BC [auth N] SDF format, chain HB [auth H] SDF format, chain JA [auth D] SDF format, chain PA [auth E] SDF format, chain Q [auth A] SDF format, chain WA [auth F] MOL2 format, chain AB [auth G] MOL2 format, chain BC [auth N] MOL2 format, chain HB [auth H] MOL2 format, chain JA [auth D] MOL2 format, chain PA [auth E] MOL2 format, chain Q [auth A] MOL2 format, chain WA [auth F] mmCIF format, chain AB [auth G] mmCIF format, chain BC [auth N] mmCIF format, chain HB [auth H] mmCIF format, chain JA [auth D] mmCIF format, chain PA [auth E] mmCIF format, chain Q [auth A] mmCIF format, chain WA [auth F]	AB [auth G] BC [auth N] HB [auth H] JA [auth D] PA [auth E] AB [auth G], BC [auth N], HB [auth H], JA [auth D], PA [auth E], Q [auth A], WA [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AB [auth G] Focus chain BC [auth N] Focus chain HB [auth H] Focus chain JA [auth D] Focus chain PA [auth E] Focus chain Q [auth A] Focus chain WA [auth F] Interactions & Density Focus chain AB [auth G] Focus chain BC [auth N] Focus chain HB [auth H] Focus chain JA [auth D] Focus chain PA [auth E] Focus chain Q [auth A] Focus chain WA [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A, B, E, F, H A, B, E, F, H, J, M	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.236 (Depositor), 0.232 (DCC)
R-Value Work: 0.196 (Depositor), 0.196 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.835	α = 90
b = 262.165	β = 90
c = 284.411	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
HKL-2000	data reduction
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-09-03

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	NS062836
National Natural Science Foundation of China (NSFC)	China	31860702