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- PDB-1u02: Crystal structure of trehalose-6-phosphate phosphatase related protein -

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Basic information

Entry
Database: PDB / ID: 1u02
TitleCrystal structure of trehalose-6-phosphate phosphatase related protein
Componentstrehalose-6-phosphate phosphatase related protein
KeywordsSTRUCTURAL GENOMICS / Phosphatase / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


trehalose-phosphatase / trehalose-phosphatase activity / trehalose biosynthetic process / magnesium ion binding
Similarity search - Function
Trehalose-6-phosphate phosphatase related protein; domain 2 / Trehalose 6-phosphate OTSB-like / Trehalose-phosphatase / Trehalose-phosphatase / HAD-superfamily hydrolase, subfamily IIB / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Alpha-Beta Plaits / Rossmann fold ...Trehalose-6-phosphate phosphatase related protein; domain 2 / Trehalose 6-phosphate OTSB-like / Trehalose-phosphatase / Trehalose-phosphatase / HAD-superfamily hydrolase, subfamily IIB / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Trehalose-6-phosphate phosphatase-related protein
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.92 Å
AuthorsKrishnamurthy, N.R. / Kumaran, D. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Protein Sci. / Year: 2006
Title: Crystal structure of trehalose-6-phosphate phosphatase-related protein: biochemical and biological implications.
Authors: Rao, K.N. / Kumaran, D. / Seetharaman, J. / Bonanno, J.B. / Burley, S.K. / Swaminathan, S.
History
DepositionJul 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: trehalose-6-phosphate phosphatase related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7746
Polymers27,5191
Non-polymers2545
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.995, 45.056, 53.391
Angle α, β, γ (deg.)90.00, 90.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein trehalose-6-phosphate phosphatase related protein


Mass: 27519.264 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: Ta1209 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HIW7
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 4000, magnesium, chloride, Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792, 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2004 / Details: mirrors
RadiationMonochromator: Silicone / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97951
ReflectionResolution: 1.92→50 Å / Num. all: 21559 / Num. obs: 21559 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 14.7
Reflection shellResolution: 1.92→1.99 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.27 / Num. unique all: 2086 / Rsym value: 0.27 / % possible all: 97.4

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Processing

Software
NameVersionClassification
CBASSdata collection
SCALEPACKdata scaling
SOLVE& sharpphasing
CNSrefinement
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.92→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2161 1034 -Random
Rwork0.1968 ---
all-21237 --
obs-21237 95 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.377 Å20 Å2-0.33 Å2
2---0.823 Å20 Å2
3---0.446 Å2
Refinement stepCycle: LAST / Resolution: 1.92→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1817 0 15 173 2005
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.27728
X-RAY DIFFRACTIONc_bond_d0.005478
LS refinement shellResolution: 1.92→1.99 Å
RfactorNum. reflection% reflection
Rfree0.2632 120 -
Rwork0.2603 --
obs-1796 97.4 %

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