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- PDB-2yyv: Crystal structure of uncharacterized conserved protein from Therm... -

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Basic information

Entry
Database: PDB / ID: 2yyv
TitleCrystal structure of uncharacterized conserved protein from Thermotoga maritima
ComponentsProbable 2-phosphosulfolactate phosphatase
KeywordsHYDROLASE / Uncharacterized conserved protein / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


2-phosphosulfolactate phosphatase / 2-phosphosulfolactate phosphatase activity / sulfopyruvate decarboxylase activity / magnesium ion binding
Similarity search - Function
putative 2-phosphosulfolactate phosphatase / ComB-like / ComB-like / ComB-like superfamily / 2-phosphosulpholactate phosphatase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Probable 2-phosphosulfolactate phosphatase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsNakagawa, N. / Nakamura, Y. / Bessho, Y. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of uncharacterized conserved protein from Thermotoga maritima
Authors: Nakagawa, N. / Nakamura, Y. / Bessho, Y. / Yokoyama, S. / Kuramitsu, S.
History
DepositionMay 2, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Nov 20, 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: Probable 2-phosphosulfolactate phosphatase
B: Probable 2-phosphosulfolactate phosphatase


Theoretical massNumber of molelcules
Total (without water)49,7792
Polymers49,7792
Non-polymers00
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-9 kcal/mol
Surface area18190 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)68.585, 72.414, 178.483
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Probable 2-phosphosulfolactate phosphatase / conserved hypothetical protein


Mass: 24889.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Plasmid: pET-21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: Q9WZQ4, 2-phosphosulfolactate phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.23 Å3/Da / Density % sol: 44.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH7.5, 10% iso-Propanol, 20% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 13, 2006 / Details: mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 52400 / % possible obs: 97.7 % / Redundancy: 7.2 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.039

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
DPSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→44.6 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 166159.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.233 5264 10.1 %RANDOM
Rwork0.221 ---
obs0.221 52076 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.7342 Å2 / ksol: 0.37434 e/Å3
Displacement parametersBiso mean: 14.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2---0.74 Å20 Å2
3---0.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.03 Å
Refinement stepCycle: LAST / Resolution: 1.65→44.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3427 0 0 252 3679
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.27 839 10.3 %
Rwork0.222 7318 -
obs--92.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top

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