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- PDB-2hw4: Crystal structure of human phosphohistidine phosphatase -

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Basic information

Entry
Database: PDB / ID: 2hw4
TitleCrystal structure of human phosphohistidine phosphatase
Components14 kDa phosphohistidine phosphatase
Keywordsstructural genomics / hydrolase / phosphohistidine / phosphatase / phpt1 / human / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


phosphohistidine phosphatase / peptidyl-histidine dephosphorylation / negative regulation of lyase activity / negative regulation of ATP citrate synthase activity / protein histidine phosphatase activity / lamellipodium organization / leading edge of lamellipodium / positive regulation of cell motility / negative regulation of T cell receptor signaling pathway / calcium channel inhibitor activity ...phosphohistidine phosphatase / peptidyl-histidine dephosphorylation / negative regulation of lyase activity / negative regulation of ATP citrate synthase activity / protein histidine phosphatase activity / lamellipodium organization / leading edge of lamellipodium / positive regulation of cell motility / negative regulation of T cell receptor signaling pathway / calcium channel inhibitor activity / protein dephosphorylation / actin filament binding / actin cytoskeleton organization / transmembrane transporter binding / nuclear body / extracellular exosome / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Janus/Ocnus / Janus / Janus superfamily / Janus/Ocnus family (Ocnus) / Pyruvoyl-Dependent Histidine Decarboxylase; Chain B / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / 14 kDa phosphohistidine phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBusam, R.D. / Thorsell, A.G. / Arrowsmith, C. / Berglund, H. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. / Graslund, S. ...Busam, R.D. / Thorsell, A.G. / Arrowsmith, C. / Berglund, H. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Holmberg Schiavone, L. / Hogbom, M. / Kotenyova, T. / Nilsson-Ehle, P. / Nordlund, P. / Nyman, T. / Ogg, D. / Stenmark, P. / Sundstrom, M. / Uppenberg, J. / Van Den Berg, S. / Weigelt, J. / Persson, C. / Hallberg, B.M. / Structural Genomics Consortium (SGC)
CitationJournal: J.Biol.Chem. / Year: 2006
Title: First structure of a eukaryotic phosphohistidine phosphatase
Authors: Busam, R.D. / Thorsell, A.G. / Flores, A. / Persson, C. / Hallberg, B.M.
History
DepositionJul 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14 kDa phosphohistidine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,95118
Polymers16,1691
Non-polymers78217
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.530, 112.530, 29.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Detailsfunctional monomer

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Components

#1: Protein 14 kDa phosphohistidine phosphatase / Phosphohistidine phosphatase 1 / Protein janus-A homolog


Mass: 16168.982 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHPT1, PHP14 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NRX4, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.9 M Sodium Formate, 0.1 M Bis-tris propane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.03313 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 26, 2006
RadiationMonochromator: Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03313 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 10665 / Num. obs: 10665 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rsym value: 0.056 / Net I/σ(I): 20.62
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 6.47 / Rsym value: 0.226 / % possible all: 88.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Se-Met MAD structure determined from other crystals

Resolution: 1.9→21.27 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.019 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22469 510 4.8 %RANDOM
Rwork0.1707 ---
all0.179 10151 --
obs0.17325 10151 97.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.399 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.02 Å20 Å2
2--0.05 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.9→21.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms985 0 0 110 1095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0211049
X-RAY DIFFRACTIONr_bond_other_d0.0030.02702
X-RAY DIFFRACTIONr_angle_refined_deg1.7741.9491395
X-RAY DIFFRACTIONr_angle_other_deg1.09231706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2585128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75624.28649
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26715175
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.97154
X-RAY DIFFRACTIONr_chiral_restr0.1220.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021171
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02215
X-RAY DIFFRACTIONr_nbd_refined0.2070.2211
X-RAY DIFFRACTIONr_nbd_other0.20.2739
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2502
X-RAY DIFFRACTIONr_nbtor_other0.0880.2574
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.267
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2650.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2580.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8011.5814
X-RAY DIFFRACTIONr_mcbond_other0.3541.5268
X-RAY DIFFRACTIONr_mcangle_it2.1532991
X-RAY DIFFRACTIONr_scbond_it3.213487
X-RAY DIFFRACTIONr_scangle_it4.2854.5404
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 25 -
Rwork0.194 625 -
obs--80.55 %

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