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- PDB-6j58: Crystal structure of human HINT1 complexing with AP4A -

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Basic information

Entry
Database: PDB / ID: 6j58
TitleCrystal structure of human HINT1 complexing with AP4A
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 MONOPHOSPHATE / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.521 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 10, 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

Downloads & links

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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)28,3963
Polymers28,0482
Non-polymers3471
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-22 kcal/mol
Surface area9480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.721, 46.422, 64.251
Angle α, β, γ (deg.)90.000, 94.900, 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: 14024.165 Da / Num. of mol.: 2
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-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.09 Å3/Da / Density % sol: 41.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / 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-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.52→25 Å / Num. obs: 35587 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 12.78 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 41.2
Reflection shellResolution: 1.52→1.57 Å / Rmerge(I) obs: 0.277 / Num. unique obs: 1790 / % possible all: 100

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Processing

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

4eqe


Resolution: 1.521→24.465 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 16.69
RfactorNum. reflection% reflection
Rfree0.1704 1754 5 %
Rwork0.1567 --
obs0.1574 35066 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 59.21 Å2 / Biso mean: 17.608 Å2 / Biso min: 6.69 Å2
Refinement stepCycle: final / Resolution: 1.521→24.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1757 0 23 288 2068
Biso mean--14.56 32.44 -
Num. residues----229
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 (%)
1.5212-1.57550.21221250.17652899302486
1.5755-1.63860.18981670.17343330349799
1.6386-1.71320.1911770.169333433520100
1.7132-1.80350.20891700.17133883558100
1.8035-1.91640.18132050.161333213526100
1.9164-2.06430.1641790.156633933572100
2.0643-2.27190.18021830.156433753558100
2.2719-2.60030.1771660.161833903556100
2.6003-3.27490.16821980.155634173615100
3.2749-24.46820.14491840.143534563640100
Refinement TLS params.Method: refined / Origin x: 13.1449 Å / Origin y: 1.0647 Å / Origin z: 16.3805 Å
111213212223313233
T0.0469 Å20.001 Å20.0047 Å2-0.0593 Å2-0.0049 Å2--0.0965 Å2
L0.3469 °20.0301 °20.0039 °2-0.877 °2-0.1042 °2--2.2528 °2
S-0.0008 Å °0.0174 Å °-0.016 Å °0.0209 Å °-0.007 Å °0.0313 Å °0.0851 Å °-0.0366 Å °0.0085 Å °
Refinement TLS groupSelection details: ALL

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