2B1R | pdb_00002b1r

X-ray structure of the sucrose-phosphatase (SPP) from Synechocystis sp.PCC6803 in complex with cellobiose

PDB DOI: https://doi.org/10.2210/pdb2B1R/pdb

Classification: HYDROLASE
Organism(s): Synechocystis sp. PCC 6803
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2005-09-16 Released: 2006-09-12
Deposition Author(s): Fieulaine, S., Lunn, J.E., Ferrer, J.-L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.198 (Depositor), 0.187 (DCC)
R-Value Work:
0.177 (Depositor), 0.187 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of a cyanobacterial sucrose-phosphatase in complex with glucose-containing disaccharides

Fieulaine, S., Lunn, J.E., Ferrer, J.-L.

(2007) Proteins 68: 796-801

PubMed: 17510968 Search on PubMed
DOI: https://doi.org/10.1002/prot.21481
Primary Citation Related Structures:
2B1Q, 2B1R, 2D2V

Organizational Affiliation

Institut de Biologie Structurale J-P. Ebel, CEA/CNRS/UJF, Grenoble, France.

Macromolecule Content

Total Structure Weight: 28.16 kDa
Atom Count: 2,215
Modeled Residue Count: 244
Deposited Residue Count: 244
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hypothetical protein slr0953	A	244	Synechocystis sp. PCC 6803	Mutation(s): 0 Gene Names: spp EC: 3.1.3.24
UniProt
Find proteins for P74325 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)) Explore P74325 Go to UniProtKB: P74325
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P74325
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	B	2		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G84824ZO GlyCosmos: G84824ZO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900005 Query on PRD_900005	B	beta-cellobiose	Oligosaccharide / Metabolism		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.198 (Depositor), 0.187 (DCC)
R-Value Work: 0.177 (Depositor), 0.187 (DCC)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.68	α = 90
b = 68.68	β = 90
c = 268.71	γ = 120

Software Package:

Software Name	Purpose
XDS	data scaling
XDS	data reduction
CNS	refinement
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2006-09-12

Deposition Author(s):

Fieulaine, S.

Lunn, J.E.

Ferrer, J.-L.

Revision History (Full details and data files)

Version 1.0: 2006-09-12
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-10-25
Changes: Data collection, Database references, Refinement description, Structure summary