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- PDB-7q2u: The crystal structure of the HINT1 Q62A mutant. -

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Basic information

Entry
Database: PDB / ID: 7q2u
TitleThe crystal structure of the HINT1 Q62A mutant.
ComponentsHistidine triad nucleotide-binding protein 1
KeywordsHYDROLASE / histidine triad nucleotide-binding protein / HINT / HIT family / Q62A mutant
Function / homology
Function and homology information


purine ribonucleotide catabolic process / adenylylsulfatase activity / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / sulfur compound metabolic process / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of calcium-mediated signaling ...purine ribonucleotide catabolic process / adenylylsulfatase activity / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / sulfur compound metabolic process / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of calcium-mediated signaling / protein kinase C binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cytoskeleton / 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 superfamily
Similarity search - Domain/homology
CACODYLATE ION / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsDolot, R.M. / Strom, A.M. / Wagner, C.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochemistry / Year: 2022
Title: Dynamic Long-Range Interactions Influence Substrate Binding and Catalysis by Human Histidine Triad Nucleotide-Binding Proteins (HINTs), Key Regulators of Multiple Cellular Processes and ...Title: Dynamic Long-Range Interactions Influence Substrate Binding and Catalysis by Human Histidine Triad Nucleotide-Binding Proteins (HINTs), Key Regulators of Multiple Cellular Processes and Activators of Antiviral ProTides.
Authors: Strom, A. / Shah, R. / Dolot, R. / Rogers, M.S. / Tong, C.L. / Wang, D. / Xia, Y. / Lipscomb, J.D. / Wagner, C.R.
History
DepositionOct 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Derived calculations / Refinement description
Category: atom_type / citation ...atom_type / citation / citation_author / refine
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.identifier_ORCID / _citation_author.name / _refine.pdbx_diffrn_id
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
CCC: Histidine triad nucleotide-binding protein 1
DDD: Histidine triad nucleotide-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8188
Polymers55,0684
Non-polymers7514
Water4,612256
1
AAA: Histidine triad nucleotide-binding protein 1
BBB: Histidine triad nucleotide-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9534
Polymers27,5342
Non-polymers4192
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-13 kcal/mol
Surface area10240 Å2
MethodPISA
2
CCC: Histidine triad nucleotide-binding protein 1
DDD: Histidine triad nucleotide-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8654
Polymers27,5342
Non-polymers3312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-10 kcal/mol
Surface area10310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.891, 112.891, 43.634
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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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: 13766.879 Da / Num. of mol.: 4 / Mutation: Q62A
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): Rosetta2 pLysS / References: UniProt: P49773, Hydrolases
#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.52 Å3/Da / Density % sol: 51.18 % / Description: elongated colorless prisms
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 16% (w/v) PEG3350, 0.2 M sodium citrate, 0.1 M sodium cacodylate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.27→43.63 Å / Num. obs: 25856 / % possible obs: 100 % / Redundancy: 13.3 % / Biso Wilson estimate: 41.5 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.078 / Net I/σ(I): 10.1
Reflection shellResolution: 2.27→2.34 Å / Redundancy: 13.7 % / Rmerge(I) obs: 1.621 / Mean I/σ(I) obs: 2 / Num. unique obs: 2340 / CC1/2: 0.748 / Rpim(I) all: 0.66 / Χ2: 0.99 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDS20190315data reduction
Aimless0.7.4data scaling
MOLREP11.7.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TW2

3tw2


Resolution: 2.27→40.733 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.21 / WRfactor Rwork: 0.154 / SU B: 7.501 / SU ML: 0.175 / Average fsc free: 0.8945 / Average fsc work: 0.9155 / Cross valid method: THROUGHOUT / ESU R: 0.251 / ESU R Free: 0.203
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2202 1305 5.05 %
Rwork0.1636 24537 -
all0.167 --
obs-25842 99.95 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 43.865 Å2
Baniso -1Baniso -2Baniso -3
1--2.047 Å20 Å20 Å2
2---2.047 Å20 Å2
3---4.094 Å2
Refinement stepCycle: LAST / Resolution: 2.27→40.733 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3572 0 42 256 3870
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133751
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163588
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.6335065
X-RAY DIFFRACTIONr_angle_other_deg1.2371.5918312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3095472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95222180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.56715634
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.851521
X-RAY DIFFRACTIONr_chiral_restr0.0760.2470
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024230
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02788
X-RAY DIFFRACTIONr_nbd_refined0.1890.2650
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.23126
X-RAY DIFFRACTIONr_nbtor_refined0.1520.21698
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21732
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2145
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1140.29
X-RAY DIFFRACTIONr_nbd_other0.1320.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.120.211
X-RAY DIFFRACTIONr_mcbond_it3.9784.3971882
X-RAY DIFFRACTIONr_mcbond_other3.9774.3981880
X-RAY DIFFRACTIONr_mcangle_it5.6096.5722356
X-RAY DIFFRACTIONr_mcangle_other5.6096.5722356
X-RAY DIFFRACTIONr_scbond_it4.5644.8281869
X-RAY DIFFRACTIONr_scbond_other4.5634.8291870
X-RAY DIFFRACTIONr_scangle_it6.9157.062709
X-RAY DIFFRACTIONr_scangle_other6.9137.0612710
X-RAY DIFFRACTIONr_lrange_it8.77350.6763835
X-RAY DIFFRACTIONr_lrange_other8.76250.5783813
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.3290.284780.2531808X-RAY DIFFRACTION99.947
2.329-2.3930.283810.2381751X-RAY DIFFRACTION100
2.393-2.4620.296970.2251707X-RAY DIFFRACTION99.9446
2.462-2.5370.288820.2171646X-RAY DIFFRACTION100
2.537-2.620.268890.2081595X-RAY DIFFRACTION100
2.62-2.7120.3870.1931546X-RAY DIFFRACTION100
2.712-2.8140.262800.1691517X-RAY DIFFRACTION100
2.814-2.9280.272820.1611434X-RAY DIFFRACTION100
2.928-3.0580.278910.1741359X-RAY DIFFRACTION100
3.058-3.2060.227570.1761333X-RAY DIFFRACTION100
3.206-3.3780.244850.1551270X-RAY DIFFRACTION100
3.378-3.5820.208580.1481189X-RAY DIFFRACTION100
3.582-3.8280.18700.1381126X-RAY DIFFRACTION100
3.828-4.1320.21490.1321063X-RAY DIFFRACTION100
4.132-4.5220.153620.125968X-RAY DIFFRACTION99.903
4.522-5.0490.147480.121889X-RAY DIFFRACTION100
5.049-5.8170.147280.152795X-RAY DIFFRACTION99.6368
5.817-7.0930.231350.168677X-RAY DIFFRACTION99.8597
7.093-9.9010.255250.153536X-RAY DIFFRACTION100
9.901-40.7330.202210.205328X-RAY DIFFRACTION99.7143

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