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- PDB-6n3y: Human Histidine Triad Nucleotide Binding Protein 1 (Hint1) with B... -

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Basic information

Entry
Database: PDB / ID: 6n3y
TitleHuman Histidine Triad Nucleotide Binding Protein 1 (Hint1) with Bound 5'-O-[(3-Indolyl)-1-Ethyl]Carbamoyl Guanosine
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
5'-O-{[2-(1H-indol-3-yl)ethyl]carbamoyl}guanosine / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsStrom, A.M. / Finzel, B.C.
CitationJournal: Acs Chem Neurosci / Year: 2019
Title: Inhibition of HINT1 Modulates Spinal Nociception and NMDA Evoked Behavior in Mice.
Authors: Shah, R.M. / Peterson, C. / Strom, A. / Dillenburg, M. / Finzel, B. / Kitto, K.F. / Fairbanks, C. / Wilcox, G. / Wagner, C.R.
History
DepositionNov 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Oct 11, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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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)28,7335
Polymers28,1922
Non-polymers5403
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-39 kcal/mol
Surface area9270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.161, 46.327, 63.896
Angle α, β, γ (deg.)90.000, 94.320, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Histidine triad nucleotide-binding protein 1 / Adenosine 5'-monophosphoramidase / Protein kinase C inhibitor 1 / Protein kinase C-interacting ...Adenosine 5'-monophosphoramidase / Protein kinase C inhibitor 1 / Protein kinase C-interacting protein 1 / PKCI-1


Mass: 14096.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HINT1, HINT, PKCI1, PRKCNH1 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta 2 pLysS BL21(DE3) / References: UniProt: P49773
#2: Chemical ChemComp-HHJ / 5'-O-{[2-(1H-indol-3-yl)ethyl]carbamoyl}guanosine


Mass: 469.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23N7O6
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 39.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.3 / Details: 100 mM MES, 35% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.578→63.714 Å / Num. obs: 27713 / % possible obs: 87.8 % / Redundancy: 3 % / Biso Wilson estimate: 13.8 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.04 / Rrim(I) all: 0.072 / Net I/σ(I): 11.3 / Num. measured all: 82943
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.578-1.5831.90.2481460.850.2170.33144.8
7.32-63.71430.033400.9980.0210.03798

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Processing

Software
NameVersionClassification
autoPROCdata scaling
PHENIX(1.13_2998)refinement
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TW2

3tw2


Resolution: 1.8→34.419 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 25.78
RfactorNum. reflection% reflection
Rfree0.2475 1038 4.95 %
Rwork0.2048 --
obs0.2069 20977 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.05 Å2 / Biso mean: 16.7384 Å2 / Biso min: 1.04 Å2
Refinement stepCycle: final / Resolution: 1.8→34.419 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1744 0 36 55 1835
Biso mean--29.32 18.49 -
Num. residues----223
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.89490.29291670.22022854302199
1.8949-2.01360.26031440.20622829297399
2.0136-2.16910.28421420.21112855299799
2.1691-2.38730.29161510.21072831298298
2.3873-2.73270.2491360.23232836297298
2.7327-3.44240.2921360.21322846298298
3.4424-34.42510.18211620.1772888305098

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