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- PDB-5km6: Human Histidine Triad Nucleotide Binding Protein 1 (hHint1) H112N... -

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Basic information

Entry
Database: PDB / ID: 5km6
TitleHuman Histidine Triad Nucleotide Binding Protein 1 (hHint1) H112N mutant Ara-A nucleoside phosphoramidate substrate 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
Chem-6US / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 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 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5622
Polymers14,0721
Non-polymers4891
Water1,65792
1
A: Histidine triad nucleotide-binding protein 1
hetero molecules

A: Histidine triad nucleotide-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1234
Polymers28,1442
Non-polymers9792
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4040 Å2
ΔGint-14 kcal/mol
Surface area9250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.163, 40.163, 144.239
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Histidine triad nucleotide-binding protein 1 / Adenosine 5'-monophosphoramidase


Mass: 14072.145 Da / Num. of mol.: 1 / Mutation: H112N
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-6US / [(2~{R},3~{S},4~{S},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-~{N}-[2-(1~{H}-indol-3-yl)ethyl]phosphonamidic acid / TpAra-Ad


Mass: 489.422 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N7O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 40.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100 mM MES, 32% 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: Apr 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→144.239 Å / Num. obs: 16559 / % possible obs: 100 % / Redundancy: 12.1 % / Biso Wilson estimate: 14.18 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.019 / Rrim(I) all: 0.065 / Net I/σ(I): 25.9 / Num. measured all: 199943
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.6-1.60512.70.3361100
7.426-144.2398.90.0351100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.17 Å38.69 Å
Translation5.17 Å38.69 Å

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KPF

1kpf


Resolution: 1.6→35.089 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 16.96
RfactorNum. reflection% reflection
Rfree0.1913 791 4.8 %
Rwork0.1716 --
obs0.1725 16477 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 45.11 Å2 / Biso mean: 16.0023 Å2 / Biso min: 6.73 Å2
Refinement stepCycle: final / Resolution: 1.6→35.089 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms860 0 34 92 986
Biso mean--11.71 25.04 -
Num. residues----111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007922
X-RAY DIFFRACTIONf_angle_d1.3761252
X-RAY DIFFRACTIONf_chiral_restr0.054135
X-RAY DIFFRACTIONf_plane_restr0.006158
X-RAY DIFFRACTIONf_dihedral_angle_d13.899342
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6-1.70020.18951410.168725232664
1.7002-1.83150.20881450.164125622707
1.8315-2.01580.17871200.162825552675
2.0158-2.30750.19091200.166425852705
2.3075-2.90690.21141370.185926362773
2.9069-35.09720.17981280.170628252953

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