2YBV | pdb_00002ybv

STRUCTURE OF RUBISCO FROM THERMOSYNECHOCOCCUS ELONGATUS

PDB DOI: https://doi.org/10.2210/pdb2YBV/pdb

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

Deposited: 2011-03-10 Released: 2012-03-28
Deposition Author(s): Terlecka, B., Wilhelmi, V., Bialek, W., Gubernator, B., Szczepaniak, A., Hofmann, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.232 (Depositor), 0.230 (DCC)
R-Value Work:
0.196 (Depositor), 0.200 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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: 537.26 kDa
Atom Count: 34,583
Modeled Residue Count: 4,256
Deposited Residue Count: 4,744
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN	A, C, E, G, I A, C, E, G, I, K, M, O	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8DIS5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL SUBUNIT	B, D, F, H, J B, D, F, H, J, L, N, P	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8DIS7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain Z [auth K] SDF format, chain Y [auth I] SDF format, chain X [auth I] SDF format, chain W [auth G] SDF format, chain V [auth G] SDF format, chain U [auth E] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain EA [auth O] SDF format, chain DA [auth O] SDF format, chain CA [auth M] SDF format, chain BA [auth M] SDF format, chain AA [auth K] MOL2 format, chain Z [auth K] MOL2 format, chain Y [auth I] MOL2 format, chain X [auth I] MOL2 format, chain W [auth G] MOL2 format, chain V [auth G] MOL2 format, chain U [auth E] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain EA [auth O] MOL2 format, chain DA [auth O] MOL2 format, chain CA [auth M] MOL2 format, chain BA [auth M] MOL2 format, chain AA [auth K] mmCIF format, chain Z [auth K] mmCIF format, chain Y [auth I] mmCIF format, chain X [auth I] mmCIF format, chain W [auth G] mmCIF format, chain V [auth G] mmCIF format, chain U [auth E] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain EA [auth O] mmCIF format, chain DA [auth O] mmCIF format, chain CA [auth M] mmCIF format, chain BA [auth M] mmCIF format, chain AA [auth K]	AA [auth K] BA [auth M] CA [auth M] DA [auth O] EA [auth O] AA [auth K], BA [auth M], CA [auth M], DA [auth O], EA [auth O], Q [auth A], R [auth A], S [auth C], T [auth C], U [auth E], V [auth G], W [auth G], X [auth I], Y [auth I], Z [auth K]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth K] Focus chain BA [auth M] Focus chain CA [auth M] Focus chain DA [auth O] Focus chain EA [auth O] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth E] Focus chain V [auth G] Focus chain W [auth G] Focus chain X [auth I] Focus chain Y [auth I] Focus chain Z [auth K] Interactions & Density Focus chain AA [auth K] Focus chain BA [auth M] Focus chain CA [auth M] Focus chain DA [auth O] Focus chain EA [auth O] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth E] Focus chain V [auth G] Focus chain W [auth G] Focus chain X [auth I] Focus chain Y [auth I] Focus chain Z [auth K]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.232 (Depositor), 0.230 (DCC)
R-Value Work: 0.196 (Depositor), 0.200 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.48	α = 90
b = 163.47	β = 108.96
c = 163.54	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-03-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-03-28
Type: Initial release
Version 1.1: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary