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- PDB-1s2o: X-Ray structure of the sucrose-phosphatase (SPP) from Synechocyst... -

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Basic information

Entry
Database: PDB / ID: 1s2o
TitleX-Ray structure of the sucrose-phosphatase (SPP) from Synechocystis sp. PCC6803 at 1.40 A resolution
Componentssucrose-phosphatase
KeywordsHYDROLASE / phosphohydrolase / HAD superfamily / sucrose / cyanobacteria
Function / homology
Function and homology information


sucrose-phosphate phosphatase / sucrose-phosphate phosphatase activity / sucrose biosynthetic process / magnesium ion binding
Similarity search - Function
Sucrose phosphatase, plant/cyanobacteria / : / Sucrose phosphatase-like domain / Sucrose-6F-phosphate phosphohydrolase / Hypothetical Protein Ta0175; Chain: A, domain 2 - #10 / HAD-superfamily hydrolase, subfamily IIB / Hypothetical Protein Ta0175; Chain: A, domain 2 / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily ...Sucrose phosphatase, plant/cyanobacteria / : / Sucrose phosphatase-like domain / Sucrose-6F-phosphate phosphohydrolase / Hypothetical Protein Ta0175; Chain: A, domain 2 - #10 / HAD-superfamily hydrolase, subfamily IIB / Hypothetical Protein Ta0175; Chain: A, domain 2 / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
sucrose-phosphate phosphatase
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsFieulaine, S. / Lunn, J.E. / Borel, F. / Ferrer, J.L.
CitationJournal: Plant Cell / Year: 2005
Title: The structure of a cyanobacterial sucrose-phosphatase reveals the sugar tongs that release free sucrose in the cell.
Authors: Fieulaine, S. / Lunn, J.E. / Borel, F. / Ferrer, J.L.
History
DepositionJan 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: sucrose-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8142
Polymers27,7901
Non-polymers241
Water6,269348
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.070, 51.760, 52.140
Angle α, β, γ (deg.)90.00, 101.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein sucrose-phosphatase / SPP


Mass: 27789.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: spp / Plasmid: pTYB2 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: P74325, sucrose-phosphate phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: NaFormate, NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM30A11.483148
SYNCHROTRONESRF ID14-120.934
Detector
TypeIDDetectorDate
MARRESEARCH1CCDOct 11, 2003
ADSC QUANTUM 42CCDSep 19, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111SADMx-ray1
2laue diamond C111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.4831481
20.9341
ReflectionResolution: 1.4→50 Å / Num. obs: 45838 / % possible obs: 96.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 12.58

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: SAD / Resolution: 1.4→20 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2 2257 -random
Rwork0.182 ---
all-47382 --
obs-45521 96.1 %-
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1920 0 1 348 2269
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.312

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