3ZXW | pdb_00003zxw

STRUCTURE OF ACTIVATED RUBISCO FROM THERMOSYNECHOCOCCUS ELONGATUS COMPLEXED WITH 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE

PDB DOI: https://doi.org/10.2210/pdb3ZXW/pdb

Classification: LYASE
Organism(s): Thermosynechococcus vestitus BP-1
Expression System: Escherichia coli DH5[alpha]
Mutation(s): No

Deposited: 2011-08-16 Released: 2012-08-29
Deposition Author(s): Terlecka, B., Wilhelmi, V., Bialek, W., Gubernator, B., Szczepaniak, A., Hofmann, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.213 (Depositor), 0.215 (DCC)
R-Value Work:
0.181 (Depositor), 0.183 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structure of Ribulose-1,5-Bisphosphate Carboxylase Oxygenase from Thermosynechococcus Elongatus

Terlecka, B., Wilhelmi, V., Bialek, W., Gubernator, B., Szczepaniak, A., Hofmann, E.

To be published.

Macromolecule Content

Total Structure Weight: 271.07 kDa
Atom Count: 18,787
Modeled Residue Count: 2,228
Deposited Residue Count: 2,372
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN	A, C, E, G	475	Thermosynechococcus vestitus BP-1	Mutation(s): 0 EC: 4.1.1.39
UniProt
Find proteins for Q8DIS5 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DIS5 Go to UniProtKB: Q8DIS5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8DIS5
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN	B, D, F, H	118	Thermosynechococcus vestitus BP-1	Mutation(s): 0 EC: 4.1.1.39
UniProt
Find proteins for Q8DIS7 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DIS7 Go to UniProtKB: Q8DIS7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8DIS7
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 Z [auth G] SDF format, chain V [auth E] SDF format, chain P [auth C] SDF format, chain J [auth A] MOL2 format, chain Z [auth G] MOL2 format, chain V [auth E] MOL2 format, chain P [auth C] MOL2 format, chain J [auth A] mmCIF format, chain Z [auth G] mmCIF format, chain V [auth E] mmCIF format, chain P [auth C] mmCIF format, chain J [auth A]	J [auth A], P [auth C], V [auth E], Z [auth G]	2-CARBOXYARABINITOL-1,5-DIPHOSPHATE C₆ H₁₄ O₁₃ P₂ ITHCSGCUQDMYAI-ZMIZWQJLSA-N		Interactions Focus chain J [auth A] Focus chain P [auth C] Focus chain V [auth E] Focus chain Z [auth G] Interactions & Density Focus chain J [auth A] Focus chain P [auth C] Focus chain V [auth E] Focus chain Z [auth G]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain X [auth E] SDF format, chain W [auth E] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain AA [auth G] MOL2 format, chain X [auth E] MOL2 format, chain W [auth E] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain AA [auth G] mmCIF format, chain X [auth E] mmCIF format, chain W [auth E] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain AA [auth G]	AA [auth G] K [auth A] L [auth A] M [auth A] N [auth A] AA [auth G], K [auth A], L [auth A], M [auth A], N [auth A], Q [auth C], R [auth C], S [auth C], T [auth C], W [auth E], X [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth E] Focus chain X [auth E] Interactions & Density Focus chain AA [auth G] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain W [auth E] Focus chain X [auth E]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Y [auth G] SDF format, chain U [auth E] SDF format, chain O [auth C] SDF format, chain I [auth A] MOL2 format, chain Y [auth G] MOL2 format, chain U [auth E] MOL2 format, chain O [auth C] MOL2 format, chain I [auth A] mmCIF format, chain Y [auth G] mmCIF format, chain U [auth E] mmCIF format, chain O [auth C] mmCIF format, chain I [auth A]	I [auth A], O [auth C], U [auth E], Y [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain O [auth C] Focus chain U [auth E] Focus chain Y [auth G] Interactions & Density Focus chain I [auth A] Focus chain O [auth C] Focus chain U [auth E] Focus chain Y [auth G]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on KCX	A, C, E, G	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.213 (Depositor), 0.215 (DCC)
R-Value Work: 0.181 (Depositor), 0.183 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.5	α = 90
b = 111.5	β = 90
c = 397	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-08-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-08-29
Type: Initial release
Version 1.1: 2018-06-27
Changes: Data collection, Derived calculations
Version 1.2: 2024-05-01
Changes: Data collection, Database references, Derived calculations, Other, Refinement description