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- PDB-6yqm: Human histidine triad nucleotide-binding protein 1 (hHINT1) compl... -

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Basic information

Entry
Database: PDB / ID: 6yqm
TitleHuman histidine triad nucleotide-binding protein 1 (hHINT1) complexed with dGMP and refined to 1.02 A
ComponentsHistidine triad nucleotide-binding protein 1
KeywordsHYDROLASE / Nucleotide binding protein
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 / 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 superfamily
Similarity search - Domain/homology
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE / DI(HYDROXYETHYL)ETHER / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.02 Å
AuthorsDolot, R.D. / Seda, A. / Nawrot, B.C.
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2021
Title: Biochemical, crystallographic and biophysical characterization of histidine triad nucleotide-binding protein 2 with different ligands including a non-hydrolyzable analog of Ap4A.
Authors: Dolot, R. / Krakowiak, A. / Kaczmarek, R. / Wlodarczyk, A. / Pichlak, M. / Nawrot, B.
History
DepositionApr 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Histidine triad nucleotide-binding protein 1
BBB: Histidine triad nucleotide-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1014
Polymers27,6482
Non-polymers4532
Water8,701483
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-23 kcal/mol
Surface area9830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.658, 46.434, 64.102
Angle α, β, γ (deg.)90.000, 94.244, 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: 13823.931 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: pSGA02 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P49773, Hydrolases
#2: Chemical ChemComp-DGP / 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 483 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.83 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 5.7 / Details: 16 % (w/v) PEG 4000, 0.1 M sodium cacodylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.02→39.963 Å / Num. obs: 116020 / % possible obs: 99.1 % / Redundancy: 3.8 % / Biso Wilson estimate: 5.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.037 / Rrim(I) all: 0.056 / Χ2: 1.04 / Net I/σ(I): 14.1
Reflection shellResolution: 1.02→1.04 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5440 / CC1/2: 0.785 / Rpim(I) all: 0.422 / Rrim(I) all: 0.63 / Χ2: 1.06 / % possible all: 93.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.7.4data scaling
MOLREP11.7.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TW2

3tw2


Resolution: 1.02→39.96 Å / Cor.coef. Fo:Fc: 0.984 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.678 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.02 / ESU R Free: 0.022
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1356 6128 5.282 %
Rwork0.1118 --
all0.113 --
obs-116016 99.056 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 11.705 Å2
Baniso -1Baniso -2Baniso -3
1--0.117 Å2-0 Å2-0.011 Å2
2---0.047 Å2-0 Å2
3---0.163 Å2
Refinement stepCycle: LAST / Resolution: 1.02→39.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1773 0 30 483 2286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0132244
X-RAY DIFFRACTIONr_bond_other_d0.0210.0172071
X-RAY DIFFRACTIONr_angle_refined_deg2.4031.6653092
X-RAY DIFFRACTIONr_angle_other_deg1.9911.6044871
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3985305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.20922.9100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.42815393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1861510
X-RAY DIFFRACTIONr_chiral_restr0.1430.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022667
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02451
X-RAY DIFFRACTIONr_nbd_refined0.3230.2569
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.22177
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21120
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1020.21093
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2730.2329
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.270.229
X-RAY DIFFRACTIONr_nbd_other0.3690.288
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2130.256
X-RAY DIFFRACTIONr_mcbond_it5.9260.9121118
X-RAY DIFFRACTIONr_mcbond_other5.9310.9121116
X-RAY DIFFRACTIONr_mcangle_it5.5241.3471457
X-RAY DIFFRACTIONr_mcangle_other5.5241.3471457
X-RAY DIFFRACTIONr_scbond_it4.5081.1171126
X-RAY DIFFRACTIONr_scbond_other4.5061.1181127
X-RAY DIFFRACTIONr_scangle_it4.8041.5951635
X-RAY DIFFRACTIONr_scangle_other4.8021.5961636
X-RAY DIFFRACTIONr_lrange_it7.01714.2132892
X-RAY DIFFRACTIONr_lrange_other7.01614.2142893
X-RAY DIFFRACTIONr_rigid_bond_restr8.28934315
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.02-1.0460.2144050.20377230.20486130.9250.92194.3690.176
1.046-1.0750.1814470.17477860.17484280.9430.94497.68630.146
1.075-1.1060.1744380.14476800.14581880.9490.9699.14510.118
1.106-1.140.144330.12574600.12679310.9680.97199.52090.102
1.14-1.1780.1333990.11872400.11976650.9730.97499.66080.095
1.178-1.2190.1254110.10970120.1174380.9770.97999.79830.088
1.219-1.2650.1183700.10168320.10272070.9810.98299.93060.083
1.265-1.3170.1223750.10165310.10269100.9780.98299.94210.082
1.317-1.3750.1193410.09763090.09866550.980.98299.92490.081
1.375-1.4420.1233220.0960200.09263660.9790.98599.6230.077
1.442-1.520.1123490.08757050.08860700.9840.98799.73640.076
1.52-1.6120.1232900.08653880.08856930.9810.98799.73650.077
1.612-1.7230.1142270.08551560.08653890.9840.98899.88870.078
1.723-1.8610.1042740.08547310.08650200.9880.9999.70120.081
1.861-2.0380.1162490.143320.10146140.9840.98799.28480.101
2.038-2.2780.1232210.10339660.10442020.9830.98499.6430.106
2.278-2.6290.1382120.10434690.10637120.9790.98499.16490.112
2.629-3.2160.1471580.11829270.1231410.9750.97898.21710.134
3.216-4.5340.1291330.11423270.11524760.9810.98399.35380.137
4.534-39.9630.251740.19212940.19414030.9460.96497.50530.246

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