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- PDB-1tj3: X-Ray structure of the Sucrose-Phosphatase (SPP) from Synechocyst... -

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Basic information

Entry
Database: PDB / ID: 1tj3
TitleX-Ray structure of the Sucrose-Phosphatase (SPP) from Synechocystis sp. PCC6803 in a closed conformation
ComponentsSucrose-Phosphatase
KeywordsHYDROLASE / phosphoydrolase / 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. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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
DepositionJun 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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_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

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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
Water2,936163
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.750, 68.750, 268.750
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Sucrose-Phosphatase


Mass: 27789.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC6803 / 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.: 163 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: sodium Formate, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 16, 2004
RadiationMonochromator: laue diamond c111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 10021 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.203 / Rsym value: 0.203 / Net I/σ(I): 14.06

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Processing

Software
NameClassification
XDSdata scaling
XDSdata reduction
EPMRphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1S2O

1s2o


Resolution: 2.8→50 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 479 -random
Rwork0.176 ---
all-10051 --
obs-9671 96.1 %-
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1946 0 1 163 2110
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.221

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