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- PDB-2p9f: Crystal structure of TTHB049 from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 2p9f
TitleCrystal structure of TTHB049 from Thermus thermophilus HB8
ComponentsAlpha-ribazole-5'-phosphate phosphatase
KeywordsISOMERASE / 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 / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 1.75 Å
AuthorsYamamoto, H. / Taketa, M. / Kageyama, Y. / 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. / Kunishima, N.
History
DepositionMar 25, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / 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
B: Alpha-ribazole-5'-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6616
Polymers39,2932
Non-polymers3684
Water7,170398
1
A: Alpha-ribazole-5'-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8313
Polymers19,6471
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-ribazole-5'-phosphate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8313
Polymers19,6471
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.810, 92.066, 110.775
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-593-

HOH

21A-603-

HOH

DetailsBiological assembly is a monomer; the asymmetric unit contains the two biological units.

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Components

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


Mass: 19646.504 Da / Num. of mol.: 2 / Mutation: L72M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q53WB3, EC: 5.4.2.1
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 55.27 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 8.3
Details: 2.75M Sodium chloride, 0.1M Tris, pH 8.3, MICROBATCH, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. all: 44012 / Num. obs: 44012 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.074 / Net I/σ(I): 6.2
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 3.3 / Num. unique all: 4374 / Rsym value: 0.262 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
CNS1.1phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 1V37

1v37


Resolution: 1.75→29.58 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2185 -RANDOM
Rwork0.2 ---
obs0.2 44007 99.8 %-
all-44096 --
Displacement parametersBiso mean: 19 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20 Å20 Å2
2---2.29 Å20 Å2
3---1.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.75→29.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2694 0 24 398 3116
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_deg0.9
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.013
RfactorNum. reflection% reflection
Rfree0.255 365 -
Rwork0.233 --
obs-7300 99.8 %

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