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- PDB-2ekz: Structural study of Project ID TTHB049 from Thermus thermophilus ... -

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Basic information

Entry
Database: PDB / ID: 2ekz
TitleStructural study of Project ID TTHB049 from Thermus thermophilus HB8 (L52M)
ComponentsAlpha-ribazole-5'-phosphate phosphatase
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / 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: 1.85 Å
AuthorsAsada, Y. / Matsuura, Y. / Ono, N. / Nakamoto, T. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Structural study of Project ID TTHB049 from Thermus thermophilus HB8 (L52M)
Authors: Asada, Y. / Matsuura, Y. / Ono, N. / Nakamoto, T. / Kunishima, N.
History
DepositionMar 26, 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 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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


Theoretical massNumber of molelcules
Total (without water)39,2932
Polymers39,2932
Non-polymers00
Water6,648369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.910, 91.976, 111.768
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
11A-270-

HOH

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Components

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


Mass: 19646.504 Da / Num. of mol.: 2 / Mutation: L52M
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): BL-21 (DE3) / References: UniProt: Q53WB3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.74 Å3/Da / Density % sol: 55.15 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 8.3
Details: 2.75M Na Chloride, pH 8.27 0.1M Tris, pH 8.3, MICROBATCH, temperature 291K

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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: Feb 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→20 Å / Num. all: 37261 / Num. obs: 37261 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 22.804 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 10.3
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 4.5 / % possible all: 99.6

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→19.64 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1845 -RAMDOM
Rwork0.198 ---
all0.2 37225 --
obs0.2 37225 99.9 %-
Displacement parametersBiso mean: 25.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å20 Å20 Å2
2---0.35 Å20 Å2
3---0.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→19.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2694 0 0 369 3063
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 1.85→1.93 Å / Rfactor Rfree error: 0.02
RfactorNum. reflection% reflection
Rfree0.29 214 -
Rwork0.239 --
obs--100 %

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