3A13 | pdb_00003a13

Crystal structure of Type III Rubisco SP4 mutant complexed with 2-CABP and activated with Ca

PDB DOI: https://doi.org/10.2210/pdb3A13/pdb

Classification: LYASE
Organism(s): Thermococcus kodakarensis KOD1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-03-25 Released: 2010-04-07
Deposition Author(s): Nishitani, Y., Fujihashi, M., Doi, T., Yoshida, S., Atomi, H., Imanaka, T., Miki, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free:
0.250 (Depositor), 0.250 (DCC)
R-Value Work:
0.205 (Depositor), 0.210 (DCC)
R-Value Observed:
0.207 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Structure-based optimization of a Type III Rubisco from a hyperthermophile

Nishitani, Y., Fujihashi, M., Doi, T., Yoshida, S., Atomi, H., Imanaka, T., Miki, K.

To be published.

Macromolecule Content

Total Structure Weight: 502.32 kDa
Atom Count: 36,193
Modeled Residue Count: 4,362
Deposited Residue Count: 4,440
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribulose bisphosphate carboxylase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	444	Thermococcus kodakarensis KOD1	Mutation(s): 5 Gene Names: rbcL, TK2290 EC: 4.1.1.39
UniProt
Find proteins for O93627 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore O93627 Go to UniProtKB: O93627
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O93627
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAP Query on CAP Download Ideal Coordinates CCD File SDF format, chain BA [auth I] SDF format, chain L [auth A] SDF format, chain P [auth C] SDF format, chain R [auth D] SDF format, chain V [auth F] SDF format, chain X [auth G] SDF format, chain Z [auth H] SDF format, chain T [auth E] SDF format, chain N [auth B] SDF format, chain DA [auth J] MOL2 format, chain BA [auth I] MOL2 format, chain L [auth A] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain V [auth F] MOL2 format, chain X [auth G] MOL2 format, chain Z [auth H] MOL2 format, chain T [auth E] MOL2 format, chain N [auth B] MOL2 format, chain DA [auth J] mmCIF format, chain BA [auth I] mmCIF format, chain L [auth A] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D] mmCIF format, chain V [auth F] mmCIF format, chain X [auth G] mmCIF format, chain Z [auth H] mmCIF format, chain T [auth E] mmCIF format, chain N [auth B] mmCIF format, chain DA [auth J]	BA [auth I] DA [auth J] L [auth A] N [auth B] P [auth C] BA [auth I], DA [auth J], L [auth A], N [auth B], P [auth C], R [auth D], T [auth E], V [auth F], X [auth G], Z [auth H]	2-CARBOXYARABINITOL-1,5-DIPHOSPHATE C₆ H₁₄ O₁₃ P₂ ITHCSGCUQDMYAI-ZMIZWQJLSA-N		Interactions Focus chain BA [auth I] Focus chain DA [auth J] Focus chain L [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Z [auth H] Interactions & Density Focus chain BA [auth I] Focus chain DA [auth J] Focus chain L [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Z [auth H]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain S [auth E] SDF format, chain CA [auth J] MOL2 format, chain S [auth E] MOL2 format, chain CA [auth J] mmCIF format, chain S [auth E] mmCIF format, chain CA [auth J]	CA [auth J], S [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CA [auth J] Focus chain S [auth E] Interactions & Density Focus chain CA [auth J] Focus chain S [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain Y [auth H] SDF format, chain W [auth G] SDF format, chain U [auth F] SDF format, chain Q [auth D] SDF format, chain O [auth C] SDF format, chain M [auth B] SDF format, chain K [auth A] SDF format, chain AA [auth I] MOL2 format, chain Y [auth H] MOL2 format, chain W [auth G] MOL2 format, chain U [auth F] MOL2 format, chain Q [auth D] MOL2 format, chain O [auth C] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] MOL2 format, chain AA [auth I] mmCIF format, chain Y [auth H] mmCIF format, chain W [auth G] mmCIF format, chain U [auth F] mmCIF format, chain Q [auth D] mmCIF format, chain O [auth C] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A] mmCIF format, chain AA [auth I]	AA [auth I] K [auth A] M [auth B] O [auth C] Q [auth D] AA [auth I], K [auth A], M [auth B], O [auth C], Q [auth D], U [auth F], W [auth G], Y [auth H]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth I] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain U [auth F] Focus chain W [auth G] Focus chain Y [auth H] Interactions & Density Focus chain AA [auth I] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain U [auth F] Focus chain W [auth G] Focus chain Y [auth H]