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- PDB-2enw: Mutant Y92H structure of TTHB049 from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 2enw
TitleMutant Y92H structure of TTHB049 from Thermus thermophilus HB8
ComponentsAlpha-ribazole-5'-phosphate phosphatase
KeywordsHYDROLASE / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


phosphatase activity / cytoplasm
Similarity search - Function
: / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha-ribazole-5'-phosphate phosphatase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsShimizu, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Mutant Y92H structure of TTHB049 from Thermus thermophilus HB8
Authors: Shimizu, K. / Taketa, M. / Kageyama, Y. / Matsuura, Y. / Kunishima, N.
History
DepositionMar 28, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-ribazole-5'-phosphate phosphatase
B: Alpha-ribazole-5'-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2993
Polymers39,2072
Non-polymers921
Water5,116284
1
A: Alpha-ribazole-5'-phosphate phosphatase


Theoretical massNumber of molelcules
Total (without water)19,6031
Polymers19,6031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-ribazole-5'-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6962
Polymers19,6031
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.974, 91.988, 110.273
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-1116-

HOH

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Components

#1: Protein Alpha-ribazole-5'-phosphate phosphatase


Mass: 19603.438 Da / Num. of mol.: 2 / Mutation: Y92H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q53WB3, adenosylcobalamin/alpha-ribazole phosphatase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 8.3
Details: 2.75M Na Chloride, 0.1M Tris, pH 8.3, Microbatch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 24, 2007 / Details: mirror
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→10 Å / Num. all: 25271 / Num. obs: 25271 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.3 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.08 / Net I/σ(I): 8.5
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 8 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 5.4 / Rsym value: 0.315 / % possible all: 99.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1V37

1v37


Resolution: 2.1→10 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2196077.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1264 5 %RANDOM
Rwork0.195 ---
obs0.195 25271 99.8 %-
all-25271 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 75.8582 Å2 / ksol: 0.476512 e/Å3
Displacement parametersBiso mean: 23.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å20 Å20 Å2
2--1.9 Å20 Å2
3----0.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2690 0 6 284 2980
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it1.92
X-RAY DIFFRACTIONc_scbond_it2.592
X-RAY DIFFRACTIONc_scangle_it3.542.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.234 182 4.4 %
Rwork0.205 3935 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4gol.paramgol.top

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