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- PDB-5ipc: Human Histidine Triad Nucleotide Binding Protein 1 (hHint1) H112N... -

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Basic information

Entry
Database: PDB / ID: 5ipc
TitleHuman Histidine Triad Nucleotide Binding Protein 1 (hHint1) H112N mutant nucleoside thiophosphoramidate substrate complex
ComponentsHistidine triad nucleotide-binding protein 1
KeywordsHYDROLASE / HINT / histidine triad / HIT
Function / homology
Function and homology information


purine ribonucleotide catabolic process / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / Regulation of MITF-M-dependent genes involved in apoptosis / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Transcriptional and post-translational regulation of MITF-M expression and activity ...purine ribonucleotide catabolic process / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / Regulation of MITF-M-dependent genes involved in apoptosis / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of calcium-mediated signaling / protein kinase C binding / cytoskeleton / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / hydrolase activity / nucleotide binding / regulation of DNA-templated transcription / signal transduction / proteolysis / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Histidine triad (HIT) protein / HIT domain / Histidine triad, conserved site / HIT domain signature. / HIT domain profile. / HIT-like domain / HIT-like / HIT family, subunit A / HIT-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-6CE / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsMaize, K.M. / Finzel, B.C.
CitationJournal: Biochemistry / Year: 2017
Title: Caught before Released: Structural Mapping of the Reaction Trajectory for the Sofosbuvir Activating Enzyme, Human Histidine Triad Nucleotide Binding Protein 1 (hHint1).
Authors: Shah, R. / Maize, K.M. / Zhou, X. / Finzel, B.C. / Wagner, C.R.
History
DepositionMar 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jul 26, 2017Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidine triad nucleotide-binding protein 1
B: Histidine triad nucleotide-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8877
Polymers28,1442
Non-polymers7435
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-22 kcal/mol
Surface area9420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.943, 46.504, 63.916
Angle α, β, γ (deg.)90.000, 94.720, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-393-

HOH

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Components

#1: Protein Histidine triad nucleotide-binding protein 1 / Adenosine 5'-monophosphoramidase


Mass: 14072.145 Da / Num. of mol.: 2 / Mutation: H112N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HINT1, HINT / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: P49773, Hydrolases
#2: Chemical ChemComp-6CE / 5'-S-[(S)-hydroxy{[2-(1H-indol-3-yl)ethyl]amino}phosphoryl]-5'-thioguanosine / TrpGMPS


Mass: 521.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N7O6PS
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.05 Å3/Da / Density % sol: 40.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 100 mM MES, 37% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→63.699 Å / Num. obs: 54978 / % possible obs: 97.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 10.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Net I/σ(I): 19.3
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.3-1.3043.20.24917165380.9440.1650.34.696.1
6.032-63.6993.10.02118445940.9980.0140.02641.797.5

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TW2

3tw2


Resolution: 1.3→33.188 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.27
RfactorNum. reflection% reflection
Rfree0.1698 2850 5.19 %
Rwork0.1518 --
obs0.1527 54965 97.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 53.15 Å2 / Biso mean: 14.7106 Å2 / Biso min: 7.14 Å2
Refinement stepCycle: final / Resolution: 1.3→33.188 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1752 0 59 228 2039
Biso mean--17.74 24.01 -
Num. residues----227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051909
X-RAY DIFFRACTIONf_angle_d0.9952592
X-RAY DIFFRACTIONf_chiral_restr0.086277
X-RAY DIFFRACTIONf_plane_restr0.005335
X-RAY DIFFRACTIONf_dihedral_angle_d13.915720
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.32240.21661230.19912539266296
1.3224-1.34650.20941470.18692579272698
1.3465-1.37240.20741600.17872569272997
1.3724-1.40040.19811420.17522562270498
1.4004-1.43080.20521340.17592603273798
1.4308-1.46410.19511590.1642585274498
1.4641-1.50070.16771570.15622558271598
1.5007-1.54130.1831620.15152568273098
1.5413-1.58670.14551360.14932630276698
1.5867-1.63790.16021590.1422611277098
1.6379-1.69640.1751350.14412611274698
1.6964-1.76430.14541340.14842639277399
1.7643-1.84460.15341250.14622637276299
1.8446-1.94190.18681650.13972588275398
1.9419-2.06350.16131210.14792643276498
2.0635-2.22280.15561530.15152600275398
2.2228-2.44640.1611360.1442631276798
2.4464-2.80030.21141380.16062599273797
2.8003-3.52740.1631330.15452650278398
3.5274-33.19910.151310.14182713284498

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