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- PDB-6j5z: Crystal structure of human HINT1 mutant complexing with AP3A -

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Basic information

Entry
Database: PDB / ID: 6j5z
TitleCrystal structure of human HINT1 mutant complexing with AP3A
ComponentsHistidine triad nucleotide-binding protein 1
KeywordsHYDROLASE / NUCLEOTIDE BINDING / REGULATION OF TRANSCRIPTION / SIGNAL TRANSDUCTION
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
ADENOSINE / ETHANESULFONIC ACID / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsWang, J. / Fang, P. / Guo, M.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China21778067 China
National Natural Science Foundation of China21778064 China
CitationJournal: Nat Commun / Year: 2019
Title: Second messenger Ap4A polymerizes target protein HINT1 to transduce signals in Fc epsilon RI-activated mast cells.
Authors: Yu, J. / Liu, Z. / Liang, Y. / Luo, F. / Zhang, J. / Tian, C. / Motzik, A. / Zheng, M. / Kang, J. / Zhong, G. / Liu, C. / Fang, P. / Guo, M. / Razin, E. / Wang, J.
History
DepositionJan 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 22, 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
C: Histidine triad nucleotide-binding protein 1
D: Histidine triad nucleotide-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4737
Polymers55,8284
Non-polymers6453
Water13,457747
1
A: Histidine triad nucleotide-binding protein 1
B: Histidine triad nucleotide-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2924
Polymers27,9142
Non-polymers3772
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-16 kcal/mol
Surface area9490 Å2
MethodPISA
2
C: Histidine triad nucleotide-binding protein 1
D: Histidine triad nucleotide-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1813
Polymers27,9142
Non-polymers2671
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-15 kcal/mol
Surface area9400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.421, 45.440, 63.922
Angle α, β, γ (deg.)86.570, 86.480, 61.350
Int Tables number1
Space group name H-MP1

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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: 13957.096 Da / Num. of mol.: 4 / Mutation: H114A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HINT1, HINT, PKCI1, PRKCNH1 / Production host: Escherichia coli (E. coli) / References: UniProt: P49773, Hydrolases
#2: Chemical ChemComp-ESA / ETHANESULFONIC ACID


Mass: 110.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O3S
#3: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 747 / 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: 2.07 Å3/Da / Density % sol: 40.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: HEPES pH 7.5, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 94352 / % possible obs: 95.4 % / Redundancy: 3.9 % / Biso Wilson estimate: 15.08 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 25.4
Reflection shellResolution: 1.3→1.35 Å / Rmerge(I) obs: 0.405 / Num. unique obs: 4285

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EQE

4eqe


Resolution: 1.3→23.867 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 19.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.17 4752 5.04 %
Rwork0.1545 89593 -
obs0.1553 94345 85.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 71.17 Å2 / Biso mean: 20.3016 Å2 / Biso min: 11.48 Å2
Refinement stepCycle: final / Resolution: 1.3→23.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3490 0 48 747 4285
Biso mean--32.59 32.52 -
Num. residues----454
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2996-1.34610.18732370.18254813505046
1.3461-1.40.19423440.18246398674261
1.4-1.46370.19744300.18548147857778
1.4637-1.54080.19584780.180595221000091
1.5408-1.63740.18285280.171199181044695
1.6374-1.76370.17465320.1674100181055096
1.7637-1.94120.17595660.1638100371060396
1.9412-2.22190.17655110.1574101801069197
2.2219-2.79860.16835730.1569102261079998
2.7986-23.87060.15855530.1385103341088799
Refinement TLS params.Method: refined / Origin x: 13.6147 Å / Origin y: 7.7621 Å / Origin z: 15.066 Å
111213212223313233
T0.148 Å20.0129 Å20.0104 Å2-0.1318 Å20.0059 Å2--0.1485 Å2
L0.1611 °20.0894 °20.1646 °2-0.0634 °20.1053 °2--0.2802 °2
S-0.0042 Å °-0.0028 Å °0.0053 Å °-0.0039 Å °0.0006 Å °0.0057 Å °-0.015 Å °-0.0075 Å °0.0062 Å °
Refinement TLS groupSelection details: ALL

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