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- PDB-1h2f: BACILLUS STEAROTHERMOPHILUS PHOE (previously known as yhfr) in co... -

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Basic information

Entry
Database: PDB / ID: 1h2f
TitleBACILLUS STEAROTHERMOPHILUS PHOE (previously known as yhfr) in complex with trivanadate
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
PHOSPHATE ION / TRIVANADATE / Phosphoglycerate mutase
Similarity search - Component
Biological speciesBACILLUS STEAROTHERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2 Å
AuthorsRigden, D.J. / Littlejohn, J.E. / Jedrzejas, M.J.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Structures of Phosphate and Trivanadate Complexes of Bacillus Stearothermophilus Phosphatase Phoe: Structural and Functional Analysis in the Cofactor-Dependent Phosphoglycerate Mutase Superfamily
Authors: Rigden, D.J. / Littlejohn, J.E. / Henderson, K. / Jedrzejas, M.J.
#1: 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.
#2: 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
DepositionAug 8, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
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 / _pdbx_entry_details.has_protein_modification

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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)24,0233
Polymers23,6481
Non-polymers3762
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.758, 55.758, 163.586
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: 23647.676 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-VA3 / TRIVANADATE


Mass: 280.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O8V3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Compound 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 (SEE REFERENCE 2 IN REMARK 1).
Has protein modificationY
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 (SEE REFERENCE 2 IN REMARK 1).

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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: 2.27 Å3/Da / Density % sol: 45.3 %
Crystal growpH: 4.5
Details: 15 % ETHYLENE GLYCOL, 85 MM SODIUM CACODYLATE PH 4.5
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110.0 mMTris-HCl1droppH7.4
21.0 mMdithiothreitol1drop
32.0 mMEDTA1drop
4150.0 mM1dropNaCl
525 mg/mlprotein1drop
625 mMAMP substrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 17334 / % possible obs: 95.2 % / Redundancy: 4.9 % / Biso Wilson estimate: 29.6 Å2 / Rmerge(I) obs: 0.155 / Net I/σ(I): 15.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 2.1 / % possible all: 88.2
Reflection
*PLUS
Lowest resolution: 50 Å
Reflection shell
*PLUS
% possible obs: 88.2 % / Mean I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: OTHER / Resolution: 2→50 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1636651.82 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: CRYSTAL WAS EXPOSED TO 50MM AMMONIUM VANADATE, 30% ETHYLENE GLYCOL, 20MM SODIUM ACETATE PH 5.0 FOR 3 DAYS BEFORE DATA COLLECTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 835 4.8 %RANDOM
Rwork0.214 ---
obs0.214 17334 95.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.1339 Å2 / ksol: 0.307577 e/Å3
Displacement parametersBiso mean: 42.7 Å2
Baniso -1Baniso -2Baniso -3
1-7.49 Å20 Å20 Å2
2--5.28 Å20 Å2
3----12.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1665 0 16 142 1823
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.711.5
X-RAY DIFFRACTIONc_mcangle_it3.412
X-RAY DIFFRACTIONc_scbond_it4.022
X-RAY DIFFRACTIONc_scangle_it4.92.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.369 76 4.9 %
Rwork0.35 1470 -
obs--86.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PO4_XPLOR_PAR.TXTPO4_XPLOR_TOP.TXT
X-RAY DIFFRACTION4NEWVO3_PAR.TXTVO3_TOP_PATCH.TXT
Refinement
*PLUS
Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.69
LS refinement shell
*PLUS
Rfactor Rfree: 0.358 / Rfactor Rwork: 0.338 / Num. reflection Rwork: 1942

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