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- PDB-6n3w: Human Histidine Triad Nucleotide Binding Protein 1 (Hint1) with B... -

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Basic information

Entry
Database: PDB / ID: 6n3w
TitleHuman Histidine Triad Nucleotide Binding Protein 1 (Hint1) with Bound 5'-O-[3-Phenyl-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 / intrinsic apoptotic signaling pathway by p53 class mediator / histone deacetylase complex / 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 / intrinsic apoptotic signaling pathway by p53 class mediator / histone deacetylase complex / 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 / cytosol / cytoplasm
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-phenylethyl)carbamoyl]guanosine / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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: 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
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)28,6233
Polymers28,1922
Non-polymers4301
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-17 kcal/mol
Surface area9480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.972, 46.210, 63.844
Angle α, β, γ (deg.)90.000, 94.740, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-392-

HOH

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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-KBJ / 5'-O-[(2-phenylethyl)carbamoyl]guanosine


Mass: 430.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H22N6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.03 Å3/Da / Density % sol: 39.5 % / Mosaicity: 0.2 °
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: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Sep 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→63.625 Å / Num. obs: 22818 / % possible obs: 99.2 % / Redundancy: 3.6 % / Biso Wilson estimate: 10.26 Å2 / Rpim(I) all: 0.049 / Rrim(I) all: 0.094 / Rsym value: 0.08 / Net I/av σ(I): 6.7 / Net I/σ(I): 13.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.75-1.843.30.3352.133300.2140.3990.33599.8
1.84-1.963.50.2612.731100.1630.3090.26199.1
1.96-2.093.70.1634.429590.0990.1920.16399.3
2.09-2.263.60.1275.727370.0780.1490.12798.8
2.26-2.473.70.0947.625290.0570.1110.09499.4
2.47-2.773.70.079322920.0490.0940.07998.9
2.77-3.23.70.05213.320390.0320.0610.05299.4
3.2-3.913.60.0416.116950.0240.0470.0497.7
3.91-5.533.60.03517.513600.0210.040.03599.6
5.53-39.7183.50.03416.27670.0210.040.03498.8

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Processing

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

3tw2


Resolution: 1.75→63.625 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.38
RfactorNum. reflection% reflection
Rfree0.1895 1108 4.87 %
Rwork0.1532 --
obs0.155 22774 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 57.28 Å2 / Biso mean: 12.1258 Å2 / Biso min: 1.17 Å2
Refinement stepCycle: final / Resolution: 1.75→63.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1756 0 31 192 1979
Biso mean--15.19 19.73 -
Num. residues----226
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061926
X-RAY DIFFRACTIONf_angle_d0.8472621
X-RAY DIFFRACTIONf_chiral_restr0.059281
X-RAY DIFFRACTIONf_plane_restr0.005346
X-RAY DIFFRACTIONf_dihedral_angle_d11.0331148
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.82970.22521560.173626662822100
1.8297-1.92610.231280.17482707283599
1.9261-2.04680.21551370.157127172854100
2.0468-2.20480.18971340.15732697283199
2.2048-2.42670.211430.15612660280397
2.4267-2.77790.18231220.16292726284899
2.7779-3.49980.19211200.14882740286099
3.4998-63.66740.1561680.13492753292199

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