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- PDB-5ed3: crystal structure of human Hint1 complexing with AP5A -

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Basic information

Entry
Database: PDB / ID: 5ed3
Titlecrystal structure of human Hint1 complexing with AP5A
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 / intrinsic apoptotic signaling pathway by p53 class mediator / histone deacetylase complex / 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 / intrinsic apoptotic signaling pathway by p53 class mediator / histone deacetylase complex / 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: 1.309 Å
AuthorsWang, J. / Fang, P. / Guo, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100136 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM106134 United States
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
DepositionOct 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Apr 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
Revision 1.4Sep 27, 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)28,6344
Polymers28,0482
Non-polymers5862
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-21 kcal/mol
Surface area9410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.454, 46.306, 64.102
Angle α, β, γ (deg.)90.000, 94.920, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-202-

EPE

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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: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 40.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG3350, HEPES

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Data collection

DiffractionMean temperature: 100 K
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: 1.309→25 Å / Num. obs: 55250 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 14.77 Å2 / Rmerge(I) obs: 0.049 / Χ2: 0.952 / Net I/av σ(I): 34.675 / Net I/σ(I): 13.8 / Num. measured all: 402430
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.31-1.365.80.27754280.76398.9
1.36-1.417.10.25654900.816100
1.41-1.487.40.20355190.848100
1.48-1.557.40.14654690.901100
1.55-1.657.50.11555420.968100
1.65-1.787.50.09654951.193100
1.78-1.967.50.06755431.148100
1.96-2.247.60.05255271.156100
2.24-2.827.60.04355851.05100
2.82-257.50.0356520.61499.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EQE

4eqe


Resolution: 1.309→24.401 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1553 2609 5.08 %
Rwork0.1463 48751 -
obs0.1468 51360 92.81 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.2 Å2 / Biso mean: 19.6974 Å2 / Biso min: 9.61 Å2
Refinement stepCycle: final / Resolution: 1.309→24.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1764 0 35 280 2079
Biso mean--18.33 34.24 -
Num. residues----228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081853
X-RAY DIFFRACTIONf_angle_d1.2722507
X-RAY DIFFRACTIONf_chiral_restr0.086267
X-RAY DIFFRACTIONf_plane_restr0.005323
X-RAY DIFFRACTIONf_dihedral_angle_d14.134694
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.309-1.33250.1753850.15331574165957
1.3325-1.35810.1698950.1621845194068
1.3581-1.38580.22851280.16852044217275
1.3858-1.4160.20261110.16922243235482
1.416-1.44890.20611160.16252448256488
1.4489-1.48510.16141270.16362612273995
1.4851-1.52530.17241630.15592708287199
1.5253-1.57020.19181400.151327622902100
1.5702-1.62080.18011670.141827342901100
1.6208-1.67870.14951650.144227412906100
1.6787-1.74590.15481450.147527592904100
1.7459-1.82540.16541440.143327652909100
1.8254-1.92160.15011320.14327712903100
1.9216-2.04190.1371490.138727642913100
2.0419-2.19950.1641550.14627692924100
2.1995-2.42060.14741380.147327762914100
2.4206-2.77050.1731380.156427952933100
2.7705-3.48890.14291560.142928002956100
3.4889-24.40550.14321550.140128412996100
Refinement TLS params.Method: refined / Origin x: 12.8569 Å / Origin y: 1.0329 Å / Origin z: 16.2614 Å
111213212223313233
T0.0945 Å20.0001 Å20.0038 Å2-0.1251 Å2-0.0034 Å2--0.133 Å2
L0.1287 °20.0142 °2-0.0188 °2-0.6644 °2-0.0633 °2--1.3464 °2
S0.0037 Å °0.0145 Å °-0.0167 Å °0.0132 Å °-0.0107 Å °0.0278 Å °0.0522 Å °-0.0361 Å °0.006 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA14 - 126
2X-RAY DIFFRACTION1allB12 - 126
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allS1 - 282
5X-RAY DIFFRACTION1allD1

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