1RBL | pdb_00001rbl

STRUCTURE DETERMINATION AND REFINEMENT OF RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE FROM SYNECHOCOCCUS PCC6301

PDB DOI: https://doi.org/10.2210/pdb1RBL/pdb

Classification: LYASE
Organism(s): Synechococcus elongatus PCC 6301
Mutation(s): No

Deposited: 1993-05-12 Released: 1994-06-22
Deposition Author(s): Newman, J., Gutteridge, S., Branden, C.-I., Jones, T.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Work:
0.200 (Depositor), 0.203 (DCC)
R-Value Observed:
0.200 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure determination and refinement of ribulose 1,5-bisphosphate carboxylase/oxygenase from Synechococcus PCC6301.

Newman, J., Branden, C.I., Jones, T.A.

(1993) Acta Crystallogr D Biol Crystallogr 49: 548-560

PubMed: 15299492 Search on PubMed
DOI: https://doi.org/10.1107/S090744499300530X
Primary Citation Related Structures:
1RBL

PubMed Abstract:
The structure of an activated quaternary complex of ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco) from Synechococcus PCC6301 has been solved by molecular replacement. The protein crystallizes in an orthorhombic P2(1)2(1)2(1) unit cell with a complete L(8)S(8) complex consisting of 4608 residues (37 680 non-hydrogen atoms) in the asymmetric unit. Data were collected both on film and image plate using synchrotron radiation; there were 218 276 unique reflections in the final 2.2 A data set. The eightfold non-crystallographic symmetry could be used both to improve map quality and to reduce the computing requirements of refinement. The coordinates were refined using strict non-crystallographic symmetry constraints. The stereochemistry of the final model is good, and the model has an R value of 20.0% for the reflections between 7 and 2.2 A.

Organizational Affiliation

Department of Molecular Biology, Swedish University of Agricultural Sciences, Biomedical Centre, Uppsala, Sweden.

Macromolecule Content

Total Structure Weight: 521.8 kDa
Atom Count: 36,988
Modeled Residue Count: 4,608
Deposited Residue Count: 4,608
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE CHAIN)	A C [auth B] E [auth C] G [auth D] I [auth E] A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F], M [auth G], O [auth H]	467	Synechococcus elongatus PCC 6301	Mutation(s): 0 EC: 4.1.1.39
UniProt
Find proteins for P00880 (Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1)) Explore P00880 Go to UniProtKB: P00880
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00880
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (SMALL CHAIN)	B [auth M] D [auth I] F [auth N] H [auth J] J [auth O] B [auth M], D [auth I], F [auth N], H [auth J], J [auth O], L [auth K], N [auth P], P [auth L]	109	Synechococcus elongatus PCC 6301	Mutation(s): 0 EC: 4.1.1.39
UniProt
Find proteins for P04716 (Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1)) Explore P04716 Go to UniProtKB: P04716
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04716
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 X [auth C] SDF format, chain U [auth B] SDF format, chain R [auth A] SDF format, chain MA [auth H] SDF format, chain JA [auth G] SDF format, chain GA [auth F] SDF format, chain DA [auth E] SDF format, chain AA [auth D] MOL2 format, chain X [auth C] MOL2 format, chain U [auth B] MOL2 format, chain R [auth A] MOL2 format, chain MA [auth H] MOL2 format, chain JA [auth G] MOL2 format, chain GA [auth F] MOL2 format, chain DA [auth E] MOL2 format, chain AA [auth D] mmCIF format, chain X [auth C] mmCIF format, chain U [auth B] mmCIF format, chain R [auth A] mmCIF format, chain MA [auth H] mmCIF format, chain JA [auth G] mmCIF format, chain GA [auth F] mmCIF format, chain DA [auth E] mmCIF format, chain AA [auth D]	AA [auth D] DA [auth E] GA [auth F] JA [auth G] MA [auth H] AA [auth D], DA [auth E], GA [auth F], JA [auth G], MA [auth H], R [auth A], U [auth B], X [auth C]	2-CARBOXYARABINITOL-1,5-DIPHOSPHATE C₆ H₁₄ O₁₃ P₂ ITHCSGCUQDMYAI-ZMIZWQJLSA-N		Interactions Focus chain AA [auth D] Focus chain DA [auth E] Focus chain GA [auth F] Focus chain JA [auth G] Focus chain MA [auth H] Focus chain R [auth A] Focus chain U [auth B] Focus chain X [auth C] Interactions & Density Focus chain AA [auth D] Focus chain DA [auth E] Focus chain GA [auth F] Focus chain JA [auth G] Focus chain MA [auth H] Focus chain R [auth A] Focus chain U [auth B] Focus chain X [auth C]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain V [auth B] SDF format, chain S [auth A] SDF format, chain NA [auth H] SDF format, chain KA [auth G] SDF format, chain HA [auth F] SDF format, chain EA [auth E] SDF format, chain BA [auth D] MOL2 format, chain Y [auth C] MOL2 format, chain V [auth B] MOL2 format, chain S [auth A] MOL2 format, chain NA [auth H] MOL2 format, chain KA [auth G] MOL2 format, chain HA [auth F] MOL2 format, chain EA [auth E] MOL2 format, chain BA [auth D] mmCIF format, chain Y [auth C] mmCIF format, chain V [auth B] mmCIF format, chain S [auth A] mmCIF format, chain NA [auth H] mmCIF format, chain KA [auth G] mmCIF format, chain HA [auth F] mmCIF format, chain EA [auth E] mmCIF format, chain BA [auth D]	BA [auth D] EA [auth E] HA [auth F] KA [auth G] NA [auth H] BA [auth D], EA [auth E], HA [auth F], KA [auth G], NA [auth H], S [auth A], V [auth B], Y [auth C]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain EA [auth E] Focus chain HA [auth F] Focus chain KA [auth G] Focus chain NA [auth H] Focus chain S [auth A] Focus chain V [auth B] Focus chain Y [auth C] Interactions & Density Focus chain BA [auth D] Focus chain EA [auth E] Focus chain HA [auth F] Focus chain KA [auth G] Focus chain NA [auth H] Focus chain S [auth A] Focus chain V [auth B] Focus chain Y [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain W [auth C] SDF format, chain T [auth B] SDF format, chain Q [auth A] SDF format, chain LA [auth H] SDF format, chain IA [auth G] SDF format, chain FA [auth F] SDF format, chain CA [auth E] MOL2 format, chain Z [auth D] MOL2 format, chain W [auth C] MOL2 format, chain T [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain LA [auth H] MOL2 format, chain IA [auth G] MOL2 format, chain FA [auth F] MOL2 format, chain CA [auth E] mmCIF format, chain Z [auth D] mmCIF format, chain W [auth C] mmCIF format, chain T [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain LA [auth H] mmCIF format, chain IA [auth G] mmCIF format, chain FA [auth F] mmCIF format, chain CA [auth E]	CA [auth E] FA [auth F] IA [auth G] LA [auth H] Q [auth A] CA [auth E], FA [auth F], IA [auth G], LA [auth H], Q [auth A], T [auth B], W [auth C], Z [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain FA [auth F] Focus chain IA [auth G] Focus chain LA [auth H] Focus chain Q [auth A] Focus chain T [auth B] Focus chain W [auth C] Focus chain Z [auth D] Interactions & Density Focus chain CA [auth E] Focus chain FA [auth F] Focus chain IA [auth G] Focus chain LA [auth H] Focus chain Q [auth A] Focus chain T [auth B] Focus chain W [auth C] Focus chain Z [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Work: 0.200 (Depositor), 0.203 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 223.9	α = 90
b = 111.9	β = 90
c = 199.7	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 1994-06-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1994-06-22
Type: Initial release
Version 1.1: 2008-03-10
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2024-06-05
Changes: Data collection, Database references, Derived calculations, Other