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- PDB-1tuo: Crystal structure of putative phosphomannomutase from Thermus The... -

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Basic information

Entry
Database: PDB / ID: 1tuo
TitleCrystal structure of putative phosphomannomutase from Thermus Thermophilus HB8
ComponentsPutative phosphomannomutase
KeywordsBIOSYNTHETIC PROTEIN / phosphomannomutase / Thermus thermophilus HB8 / Biosynthesis of alginate / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


intramolecular phosphotransferase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Alpha-D-phosphohexomutase, C-terminal / Phosphoglucomutase/phosphomannomutase, C-terminal domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 / Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 / Alpha-D-phosphohexomutase, C-terminal domain / Alpha-D-phosphohexomutase superfamily / Alpha-D-phosphohexomutase, alpha/beta/alpha domain II / Alpha-D-phosphohexomutase, alpha/beta/alpha domain III / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III ...Alpha-D-phosphohexomutase, C-terminal / Phosphoglucomutase/phosphomannomutase, C-terminal domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 / Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 / Alpha-D-phosphohexomutase, C-terminal domain / Alpha-D-phosphohexomutase superfamily / Alpha-D-phosphohexomutase, alpha/beta/alpha domain II / Alpha-D-phosphohexomutase, alpha/beta/alpha domain III / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III / Alpha-D-phosphohexomutase, alpha/beta/alpha domain I / Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III / Alpha-D-phosphohexomutase, C-terminal domain superfamily / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I / TATA-Binding Protein / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoglucomutase/phosphomannomutase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsMisaki, S. / Suzuki, S. / Fujimoto, S. / Sakurai, M. / Kobayashi, M. / Nishijima, K. / Kunishima, N. / Sugawara, M. / Kuroishi, C. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of putative phosphomannomutase from Thermus Thermophilus HB8
Authors: Misaki, S. / Suzuki, S. / Fujimoto, S. / Sakurai, M. / Kobayashi, M. / Nishijima, K. / Kunishima, N. / Sugawara, M. / Kuroishi, C.
History
DepositionJun 25, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative phosphomannomutase


Theoretical massNumber of molelcules
Total (without water)50,3111
Polymers50,3111
Non-polymers00
Water5,044280
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.610, 55.048, 83.763
Angle α, β, γ (deg.)90.00, 108.76, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative phosphomannomutase


Mass: 50310.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pETIIa / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SKJ3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.2 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 4.4
Details: litium sulfate 0.5M, Na acetate 0.1M, pH 4.4, MICRO BATCH, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32B2 / Wavelength: 0.97121, 0.97920, 0.98699
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Feb 29, 2004
RadiationMonochromator: MIRROR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.971211
20.97921
30.986991
ReflectionResolution: 1.7→50 Å / Num. all: 50770 / Num. obs: 50270 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 35.32 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 19.2
Reflection shellResolution: 1.7→50 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.036 / Mean I/σ(I) obs: 19.2 / Num. unique all: 50770 / % possible all: 99.4

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNXrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.7→30 Å / Isotropic thermal model: Isotropic / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2505 -RANDAM
Rwork0.221 ---
all-50770 --
obs-50270 99 %-
Displacement parametersBiso mean: 35.32 Å2
Baniso -1Baniso -2Baniso -3
1--1.316 Å20 Å2-1.864 Å2
2--2.759 Å20 Å2
3----1.444 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3346 0 0 280 3626
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d1.133
X-RAY DIFFRACTIONc_angle_deg1.756
LS refinement shellResolution: 1.7→1.76 Å
RfactorNum. reflection% reflection
Rwork0.39 --
obs-4955 97.7 %

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