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- PDB-5km2: Human Histidine Triad Nucleotide Binding Protein 1 (hHint1) CMP c... -

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Basic information

Entry
Database: PDB / ID: 5km2
TitleHuman Histidine Triad Nucleotide Binding Protein 1 (hHint1) CMP catalytic product 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
CYTIDINE-5'-MONOPHOSPHATE / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 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)28,6435
Polymers28,1922
Non-polymers4513
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-37 kcal/mol
Surface area9440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.463, 46.208, 64.108
Angle α, β, γ (deg.)90.000, 94.490, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-404-

HOH

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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-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.05 Å3/Da / Density % sol: 40.14 % / Mosaicity: 0.1 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1 / Details: 100 mM MES, 38% PEG 8000,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Sep 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→63.911 Å / Num. obs: 62505 / % possible obs: 98.7 % / Redundancy: 3.4 % / Biso Wilson estimate: 7.93 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.25-1.272.50.247187.7
6.85-63.913.10.022183.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.9data scaling
PHASER2.6.0phasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TW2

3tw2


Resolution: 1.25→63.911 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.59
RfactorNum. reflection% reflection
Rfree0.1733 3100 4.96 %
Rwork0.1567 --
obs0.1575 62472 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 58.09 Å2 / Biso mean: 12.1412 Å2 / Biso min: 3.89 Å2
Refinement stepCycle: final / Resolution: 1.25→63.911 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 0 49 276 2087
Biso mean--13.46 22.14 -
Num. residues----227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061972
X-RAY DIFFRACTIONf_angle_d1.1962689
X-RAY DIFFRACTIONf_chiral_restr0.08288
X-RAY DIFFRACTIONf_plane_restr0.005352
X-RAY DIFFRACTIONf_dihedral_angle_d13.4747
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.25-1.26950.23041120.2062382249487
1.2695-1.29040.21061520.19692518267093
1.2904-1.31260.20171470.18482681282899
1.3126-1.33650.22711350.187527442879100
1.3365-1.36220.17551410.178327132854100
1.3622-1.390.21281410.178527122853100
1.39-1.42020.21351340.179427332867100
1.4202-1.45330.21791330.175327252858100
1.4533-1.48960.17851420.162327142856100
1.4896-1.52990.18311640.160727272891100
1.5299-1.57490.16941360.154927042840100
1.5749-1.62570.17641610.150727212882100
1.6257-1.68380.16011360.15427412877100
1.6838-1.75130.17361510.152527022853100
1.7513-1.8310.17551160.152227642880100
1.831-1.92750.14451170.147427572874100
1.9275-2.04830.15821320.147127352867100
2.0483-2.20640.16711720.14722712288499
2.2064-2.42850.15911710.147427092880100
2.4285-2.77990.16471600.16052729288999
2.7799-3.50240.18281140.1542780289499
3.5024-63.99480.15731330.14262669280294

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