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- PDB-5km4: Human Histidine Triad Nucleotide Binding Protein 1 (hHint1)-5-Iod... -

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Basic information

Entry
Database: PDB / ID: 5km4
TitleHuman Histidine Triad Nucleotide Binding Protein 1 (hHint1)-5-Iodo-UMP complex
ComponentsHistidine triad nucleotide-binding protein 1
KeywordsHYDROLASE / HINT / histidine triad / HIT
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
5-IODOURIDINE-5'-MONOPHOSPHATE / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMaize, K.M. / Finzel, B.C.
CitationJournal: Mol. Pharm. / Year: 2017
Title: A Crystal Structure Based Guide to the Design of Human Histidine Triad Nucleotide Binding Protein 1 (hHint1) Activated ProTides.
Authors: Maize, K.M. / Shah, R. / Strom, A. / Kumarapperuma, S. / Zhou, A. / Wagner, C.R. / Finzel, B.C.
History
DepositionJun 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Database references / Category: citation_author
Revision 1.2Oct 18, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 15, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _citation.country / _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)28,6423
Polymers28,1922
Non-polymers4501
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-27 kcal/mol
Surface area9540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.852, 46.309, 63.817
Angle α, β, γ (deg.)90.000, 93.980, 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


Mass: 14096.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HINT1, HINT / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 pLysS / References: UniProt: P49773, Hydrolases
#2: Chemical ChemComp-IU / 5-IODOURIDINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 450.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12IN2O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.06 Å3/Da / Density % sol: 40.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: 100 mM MES, 34-39% PEG 8000,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→39.907 Å / Num. obs: 44339 / % possible obs: 97.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 10.46 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 12.8 / Num. measured all: 140360
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique all% possible all
1.4-1.4053.20.228143244299.5
6.489-39.9073.30.034155047096.1

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.15data extraction
PHENIXrefinement
REFMACrefinement
PHASERphasing
SCALAdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TW2

3tw2


Resolution: 1.4→32.468 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2004 2163 4.9 %
Rwork0.1754 42009 -
obs0.1767 44172 97.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.45 Å2 / Biso mean: 13.6327 Å2 / Biso min: 5.17 Å2
Refinement stepCycle: final / Resolution: 1.4→32.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 0 22 252 2036
Biso mean--13.07 21.87 -
Num. residues----227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071868
X-RAY DIFFRACTIONf_angle_d1.22537
X-RAY DIFFRACTIONf_chiral_restr0.055274
X-RAY DIFFRACTIONf_plane_restr0.006330
X-RAY DIFFRACTIONf_dihedral_angle_d13.341707
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.43260.21641230.196328732996100
1.4326-1.46840.28931600.22022786294699
1.4684-1.50810.26581290.20392779290897
1.5081-1.55250.21491260.17772847297398
1.5525-1.60260.17561500.15628342984100
1.6026-1.65990.17871300.159328703000100
1.6599-1.72630.19531530.163328573010100
1.7263-1.80490.18781620.16882815297799
1.8049-1.90.20481490.18732816296597
1.9-2.0190.25571470.21632604275191
2.019-2.17490.21261560.17652810296698
2.1749-2.39370.24291270.19532629275691
2.3937-2.73990.18551580.17742805296398
2.7399-3.45140.19271440.16672847299198
3.4514-32.47640.15491490.14932837298695

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