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- PDB-6b42: Human Histidine Triad Nucleotide Binding Protein 1 (hHint1) 2'-de... -

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Basic information

Entry
Database: PDB / ID: 6b42
TitleHuman Histidine Triad Nucleotide Binding Protein 1 (hHint1) 2'-deoxy-AMP complex at 1.13A resolution
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
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.13 Å
AuthorsMaize, K.M. / Finzel, B.C.
Funding support United States, 2items
OrganizationGrant numberCountry
Minnesota Dept. of Employment and Economic DevelopmentSPAP-06-0014-P-FY07 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM08700 United States
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
DepositionSep 25, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionOct 18, 2017ID: 5KM7
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 1.2Dec 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.country / _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4272
Polymers14,0961
Non-polymers3311
Water2,540141
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)28,8554
Polymers28,1922
Non-polymers6622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5060 Å2
ΔGint-28 kcal/mol
Surface area9770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.738, 39.738, 141.133
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 / 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: 14096.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HINT1, HINT, PKCI1, PRKCNH1 / Plasmid: PMCSG9 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA 2 PLYSS / References: UniProt: P49773
#2: Chemical ChemComp-D5M / 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE


Mass: 331.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 1.98 Å3/Da / Density % sol: 37.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: 100 MM MES, 33% 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 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.13→70.566 Å / Num. obs: 43018 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 10.6 % / Biso Wilson estimate: 9.71 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.074 / Net I/σ(I): 16.9
Reflection shellResolution: 1.13→1.134 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 350 / CC1/2: 0.75 / % possible all: 79.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.22data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AV5

1av5


Resolution: 1.13→35.283 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.99
RfactorNum. reflection% reflection
Rfree0.1599 2154 5.02 %
Rwork0.154 --
obs0.1543 42912 98.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 50.34 Å2 / Biso mean: 12.4083 Å2 / Biso min: 5.17 Å2
Refinement stepCycle: final / Resolution: 1.13→35.283 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms874 0 34 141 1049
Biso mean--8.51 21.83 -
Num. residues----113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006960
X-RAY DIFFRACTIONf_angle_d1.3711310
X-RAY DIFFRACTIONf_chiral_restr0.079142
X-RAY DIFFRACTIONf_plane_restr0.005168
X-RAY DIFFRACTIONf_dihedral_angle_d12.895369
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1301-1.15640.24011250.24212219234483
1.1564-1.18530.22281340.21472561269595
1.1853-1.21740.2111440.193427132857100
1.2174-1.25320.21521350.177527082843100
1.2532-1.29370.17681470.173326932840100
1.2937-1.33990.15181420.160227252867100
1.3399-1.39350.15821440.154827092853100
1.3935-1.4570.14231490.151827322881100
1.457-1.53380.16611420.14827572899100
1.5338-1.62990.16241270.138927402867100
1.6299-1.75570.14321420.140727652907100
1.7557-1.93240.15661640.141127612925100
1.9324-2.2120.15951600.13727932953100
2.212-2.78670.14931510.147228382989100
2.7867-35.30040.14861480.156530443192100

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