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- PDB-2p2y: Crystal structure of TTHB049 from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 2p2y
TitleCrystal 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 / FOURIER SYNTHESIS / Resolution: 1.95 Å
AuthorsSugahara, M. / Morikawa, Y. / Taketa, M. / Matsuura, Y. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of TTHB049 from Thermus thermophilus HB8
Authors: Sugahara, M. / Morikawa, Y. / Taketa, M. / Matsuura, Y. / Kunishima, N.
History
DepositionMar 8, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6822
Polymers19,6471
Non-polymers351
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.592, 42.592, 156.848
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe biological assembly is a monomer in the asymmetric unit.

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Components

#1: Protein Alpha-ribazole-5'-phosphate phosphatase / TTHB049 protein


Mass: 19646.504 Da / Num. of mol.: 1 / Mutation: L5M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET-11A / 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 1.81 Å3/Da / Density % sol: 32.01 %
Crystal growTemperature: 295 K / Method: oil micro batch / pH: 4.8
Details: 2.75M NaCl, 0.1M citrate, pH 4.8, oil micro batch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 27, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. all: 11290 / Num. obs: 11290 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.04 / Net I/σ(I): 15.3
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.119 / Mean I/σ(I) obs: 9.7 / Num. unique all: 1080 / Rsym value: 0.115 / % possible all: 99

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1v7q

1v7q


Resolution: 1.95→19.83 Å / Isotropic thermal model: Anisotrop / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 546 -RANDOM
Rwork0.225 ---
obs0.225 11227 99.7 %-
all-11227 --
Displacement parametersBiso mean: 28.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.27 Å20 Å20 Å2
2--2.27 Å20 Å2
3----4.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.95→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1343 0 1 158 1502
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.007
X-RAY DIFFRACTIONc_bond_d1.4

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