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- PDB-2nmm: Crystal structure of human phosphohistidine phosphatase. Northeas... -

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Basic information

Entry
Database: PDB / ID: 2nmm
TitleCrystal structure of human phosphohistidine phosphatase. Northeast Structural Genomics Consortium target HR1409
Components14 kDa phosphohistidine phosphatase
KeywordsHYDROLASE / NESG Q9H0Y3 human phosphohistidine phosphatase / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
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
14 kDa phosphohistidine phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsKuzin, A.P. / Abashidze, M. / Forouhar, F. / Seetharaman, J. / Kent, C. / Fang, Y. / Cunningham, K. / Conover, K. / Ma, L.C. / Xiao, R. ...Kuzin, A.P. / Abashidze, M. / Forouhar, F. / Seetharaman, J. / Kent, C. / Fang, Y. / Cunningham, K. / Conover, K. / Ma, L.C. / Xiao, R. / Acton, T. / Montelione, G. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of human phosphohistidine phosphatase. Northeast Structural Genomics Consortium target HR1409
Authors: Kuzin, A.P. / Abashidze, M. / Forouhar, F. / Seetharaman, J. / Kent, C. / Fang, Y. / Cunningham, K. / Conover, K. / Ma, L.C. / Xiao, R. / Acton, T. / Montelione, G. / Tong, L. / Hunt, J.F.
History
DepositionOct 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: 14 kDa phosphohistidine phosphatase
B: 14 kDa phosphohistidine phosphatase
C: 14 kDa phosphohistidine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4219
Polymers45,8443
Non-polymers5766
Water64936
1
A: 14 kDa phosphohistidine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4743
Polymers15,2811
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: 14 kDa phosphohistidine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4743
Polymers15,2811
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: 14 kDa phosphohistidine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4743
Polymers15,2811
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-139 kcal/mol
Surface area16340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.685, 60.088, 79.299
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 15281.453 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHPT1, PHP14 / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic
References: UniProt: Q9NRX4, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.2 Å3/Da / Density % sol: 44.08 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2M Ammonium Sulfate, 50 mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97904, 0.97926, 0.96790
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 11, 2006 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979041
20.979261
30.96791
ReflectionResolution: 2.65→50 Å / Num. obs: 18092 / % possible obs: 79.4 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 9.9 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 14.8
Reflection shellResolution: 2.65→2.74 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 4.6 / % possible all: 82.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→19.91 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 125171.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used for phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.261 742 4.9 %RANDOM
Rwork0.194 ---
obs0.194 15248 71.1 %-
all-18092 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 15.607 Å2 / ksol: 0.341695 e/Å3
Displacement parametersBiso mean: 20.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.94 Å20 Å20 Å2
2--2.49 Å20 Å2
3----0.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2641 0 30 36 2707
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.365 92 4.2 %
Rwork0.246 2092 -
obs--61.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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