7TXV | pdb_00007txv

Cyanophycin synthetase 1 from Synechocystis sp. UTEX2470 E82Q with ATP and 16x(Asp-Arg)

PDB DOI: https://doi.org/10.2210/pdb7TXV/pdb
EM Map EMD-26161: EMDB EMDataResource

Classification: LIGASE
Organism(s): Synechocystis sp. PCC 6714, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-02-09 Released: 2022-06-01
Deposition Author(s): Sharon, I., Grogg, M., Hilvert, D., Schmeing, T.M.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

A cryptic third active site in cyanophycin synthetase creates primers for polymerization

Sharon, I., Pinus, S., Grogg, M., Moitessier, N., Hilvert, D., Schmeing, T.M.

(2022) Nat Commun 13: 3923

DOI: https://doi.org/10.1038/s41467-022-31542-7

Macromolecule Content

Total Structure Weight: 422.61 kDa
Atom Count: 27,648
Modeled Residue Count: 3,528
Deposited Residue Count: 3,644
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyanophycin synthase	A, B, C, D	879	Synechocystis sp. PCC 6714	Mutation(s): 1 Gene Names: cphA, D082_30240 EC: 6.3.2.29 (PDB Primary Data), 6.3.2.30 (PDB Primary Data)
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
16x(Asp-Arg)	E, F, G, H, I E, F, G, H, I, J, K, L	16	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain GA [auth C] SDF format, chain MA [auth D] SDF format, chain NA [auth D] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain MA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] mmCIF format, chain FA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain MA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B]	FA [auth C] GA [auth C] MA [auth D] NA [auth D] R [auth A] FA [auth C], GA [auth C], MA [auth D], NA [auth D], R [auth A], S [auth A], Y [auth B], Z [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain FA [auth C] Focus chain GA [auth C] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain R [auth A] Focus chain S [auth A] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain FA [auth C] Focus chain GA [auth C] Focus chain MA [auth D] Focus chain NA [auth D] Focus chain R [auth A] Focus chain S [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain EA [auth C] SDF format, chain LA [auth D] SDF format, chain Q [auth A] SDF format, chain X [auth B] MOL2 format, chain EA [auth C] MOL2 format, chain LA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain X [auth B] mmCIF format, chain EA [auth C] mmCIF format, chain LA [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain X [auth B]	EA [auth C], LA [auth D], Q [auth A], X [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain EA [auth C] Focus chain LA [auth D] Focus chain Q [auth A] Focus chain X [auth B] Interactions & Density Focus chain EA [auth C] Focus chain LA [auth D] Focus chain Q [auth A] Focus chain X [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain HA [auth D] SDF format, chain IA [auth D] SDF format, chain JA [auth D] SDF format, chain KA [auth D] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain HA [auth D] MOL2 format, chain IA [auth D] MOL2 format, chain JA [auth D] MOL2 format, chain KA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain HA [auth D] mmCIF format, chain IA [auth D] mmCIF format, chain JA [auth D] mmCIF format, chain KA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] HA [auth D] AA [auth C], BA [auth C], CA [auth C], DA [auth C], HA [auth D], IA [auth D], JA [auth D], KA [auth D], M [auth A], N [auth A], O [auth A], P [auth A], T [auth B], U [auth B], V [auth B], W [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain HA [auth D] Focus chain IA [auth D] Focus chain JA [auth D] Focus chain KA [auth D] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
7ID Query on 7ID	E, F, G, H, I E, F, G, H, I, J, K, L	L-PEPTIDE LINKING	C₁₀ H₁₉ N₅ O₅		ASP

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-06-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	178084

Revision History (Full details and data files)

Version 1.0: 2022-06-01
Type: Initial release
Version 1.1: 2022-07-13
Changes: Database references
Version 1.2: 2024-10-23
Changes: Data collection, Derived calculations, Structure summary