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- PDB-6j53: Crystal structure of human HINT1 complexing with ATP -

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Basic information

Entry
Database: PDB / ID: 6j53
TitleCrystal structure of human HINT1 complexing with ATP
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 / 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 ...purine ribonucleotide catabolic process / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / 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 / 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
ADENOSINE MONOPHOSPHATE / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 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

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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
Water6,503361
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-23 kcal/mol
Surface area9340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.586, 46.501, 63.916
Angle α, β, γ (deg.)90.000, 94.390, 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 / Adenosine monophosphate


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


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.08 Å3/Da / Density % sol: 40.74 %
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: 35501 / % possible obs: 99.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 9.54 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 40.5
Reflection shellResolution: 1.52→1.55 Å / Rmerge(I) obs: 0.108 / Num. unique obs: 1255 / % possible all: 99.9

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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: 1.52→23.843 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1692 1776 5 %
Rwork0.1511 33723 -
obs0.152 35499 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 52.73 Å2 / Biso mean: 14.4777 Å2 / Biso min: 4.44 Å2
Refinement stepCycle: final / Resolution: 1.52→23.843 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1760 0 23 361 2144
Biso mean--10.58 28.6 -
Num. residues----228
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 (%)
1.52-1.57430.19461830.154733213504100
1.5743-1.63740.17441540.149433683522100
1.6374-1.71190.18771680.144533603528100
1.7119-1.80210.16561930.145133463539100
1.8021-1.9150.16591710.147333743545100
1.915-2.06270.17531670.148333733540100
2.0627-2.27020.17281820.151333733555100
2.2702-2.59830.18021870.161833703557100
2.5983-3.27230.18551910.156633973588100
3.2723-23.84640.14111800.14673441362199
Refinement TLS params.Method: refined / Origin x: 13.2023 Å / Origin y: 1.0436 Å / Origin z: 16.2709 Å
111213212223313233
T0.0422 Å2-0.0004 Å20.0042 Å2-0.0558 Å2-0.0023 Å2--0.0701 Å2
L0.1868 °20.0317 °20.0606 °2-0.634 °20.0495 °2--1.3707 °2
S0.007 Å °0.0052 Å °-0.0095 Å °0.045 Å °-0.0129 Å °0.0082 Å °0.0561 Å °-0.0286 Å °0.0046 Å °
Refinement TLS groupSelection details: ALL

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