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- PDB-1ebb: Bacillus stearothermophilus YhfR -

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Basic information

Entry
Database: PDB / ID: 1ebb
TitleBacillus stearothermophilus YhfR
ComponentsPHOSPHATASE
KeywordsHYDROLASE / BROAD SPECIFICITY PHOSPHATASE / DPGM HOMOLOG
Function / homology
Function and homology information


phosphatase activity / cytoplasm
Similarity search - Function
: / 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
Phosphoglycerate mutase
Similarity search - Component
Biological speciesBACILLUS STEAROTHERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRigden, D.J. / Jedrzejas, M.J.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Structure and Mechanism of Action of a Cofactor-Dependent Phosphoglycerate Mutase Homolog from Bacillus Stearothermophilus with Broad Specificity Phosphatase Activity.
Authors: Rigden, D.J. / Mello, L.V. / Setlow, P. / Jedrzejas, M.J.
#1: Journal: Protein Sci. / Year: 2001
Title: A Cofactor-Dependent Phosphoglycerate Mutase Homolog from Bacillus Stearothermophilus is Actually a Broad Specificity Phosphatase
Authors: Rigden, D.J. / Bagyan, I. / Lamani, E. / Setlow, P. / Jedrzejas, M.J.
History
DepositionJul 24, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 11, 2002Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2011Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8199
Polymers23,0621
Non-polymers7578
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.200, 55.200, 164.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein PHOSPHATASE / YHFR


Mass: 23062.006 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS STEAROTHERMOPHILUS (bacteria) / Plasmid: PS3297 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9ALU0
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SWISSPROT ENTRY Q9ALU0 IDENTIFIES THIS PROTEIN AS A PHOSPHOGLYCERATE MUTASE. THE PROTEIN ...THE SWISSPROT ENTRY Q9ALU0 IDENTIFIES THIS PROTEIN AS A PHOSPHOGLYCERATE MUTASE. THE PROTEIN STUDIED IS A HOMOLOG OF PHOSPHOGLYCERATE MUTASE BUT HAS NO MUTASE ACTIVITY. THE MOLECULE DOES SHOW PHOSPHATASE ACTIVITY.

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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: 2.72 Å3/Da / Density % sol: 54 %
Crystal growpH: 8
Details: 45 % POLYETHYLENE GLYCOL 4,000, 120 MM LITHIUM SULFATE, 20 MM TRIS.HCL BUFFER, PH 8.0
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
210 mMTris-HCl1droppH7.4
31 mMdithiothreitol1drop
42 mMEDTA1drop
5150 mM1dropNaCl
645 %(w/v)PEG40001reservoir
7120 mMlithium sulfate1reservoir
820 mMTris-HCl1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.1
DetectorType: OXFORD / Detector: CCD / Date: Jan 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→45.83 Å / Num. obs: 11896 / % possible obs: 99.5 % / Redundancy: 12.2 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 19.5
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 1.3 / % possible all: 98.8
Reflection
*PLUS
Lowest resolution: 50 Å
Reflection shell
*PLUS
% possible obs: 98.8 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1TIP, 5PGM +HOMOLOGY MODEL

1tip

5pgm


Resolution: 2.3→45.83 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1587969.35 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.263 599 5 %RANDOM
Rwork0.23 ---
obs0.23 11896 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.5009 Å2 / ksol: 0.365671 e/Å3
Displacement parametersBiso mean: 54 Å2
Baniso -1Baniso -2Baniso -3
1-9.05 Å20 Å20 Å2
2--12.53 Å20 Å2
3----21.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.3→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1623 0 43 33 1699
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.071.5
X-RAY DIFFRACTIONc_mcangle_it3.212
X-RAY DIFFRACTIONc_scbond_it3.582
X-RAY DIFFRACTIONc_scangle_it5.22.5
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.369 80 5.8 %
Rwork0.337 1306 -
obs--96.7 %
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_XPLOR_PAR.TXTGOL_XPLOR_TOP.TXT
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / Rfactor obs: 0.23 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8
LS refinement shell
*PLUS
Rfactor obs: 0.337

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