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- PDB-5km0: Human Histidine Triad Nucleotide Binding Protein 1 (hHint) IMP complex -

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Basic information

Entry
Database: PDB / ID: 5km0
TitleHuman Histidine Triad Nucleotide Binding Protein 1 (hHint) IMP complex
ComponentsHistidine triad nucleotide-binding protein 1
KeywordsHYDROLASE / HINT / histidine triad / HIT
Function / homology
Function and homology information


purine ribonucleotide catabolic process / adenylylsulfatase activity / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / sulfur compound metabolic process / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of calcium-mediated signaling ...purine ribonucleotide catabolic process / adenylylsulfatase activity / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / sulfur compound metabolic process / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of calcium-mediated signaling / protein kinase C binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / cytoskeleton / hydrolase activity / nucleotide binding / regulation of DNA-templated transcription / signal transduction / proteolysis / extracellular exosome / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
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
INOSINIC ACID / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.533 Å
AuthorsMaize, K.M. / Finzel, B.C.
Funding support United States, 1items
OrganizationGrant numberCountry
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
DepositionJun 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Author supporting evidence / Database references / Category: citation_author / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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 1.4Dec 25, 2019Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.country / _pdbx_audit_support.funding_organization
Revision 1.5Sep 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
B: Histidine triad nucleotide-binding protein 1
A: Histidine triad nucleotide-binding protein 1
C: Histidine triad nucleotide-binding protein 1
D: Histidine triad nucleotide-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0816
Polymers56,3854
Non-polymers6962
Water11,548641
1
B: Histidine triad nucleotide-binding protein 1
A: Histidine triad nucleotide-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5413
Polymers28,1922
Non-polymers3481
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-24 kcal/mol
Surface area9400 Å2
MethodPISA
2
C: Histidine triad nucleotide-binding protein 1
D: Histidine triad nucleotide-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5413
Polymers28,1922
Non-polymers3481
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-24 kcal/mol
Surface area9370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.325, 89.589, 46.372
Angle α, β, γ (deg.)90.000, 90.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 14096.188 Da / Num. of mol.: 4
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-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 641 / 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: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: 100 mM MES, 34% 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: 1.533→64.325 Å / Num. obs: 77524 / % possible obs: 98.5 % / Redundancy: 3.2 % / Biso Wilson estimate: 12.33 Å2 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.533-1.5382.30.309183
7.113-89.58930.058198.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
PHASERphasing
SCALAdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1kpc

1kpc


Resolution: 1.533→41.182 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 24.03
RfactorNum. reflection% reflection
Rfree0.2233 3907 5.04 %
Rwork0.1881 --
obs0.1899 77462 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 57.28 Å2 / Biso mean: 17.7118 Å2 / Biso min: 7.1 Å2
Refinement stepCycle: final / Resolution: 1.533→41.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3470 0 46 641 4157
Biso mean--17.59 27.34 -
Num. residues----451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063652
X-RAY DIFFRACTIONf_angle_d1.1084957
X-RAY DIFFRACTIONf_chiral_restr0.046541
X-RAY DIFFRACTIONf_plane_restr0.006639
X-RAY DIFFRACTIONf_dihedral_angle_d13.6851353
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5327-1.55140.3031150.29412273238885
1.5514-1.5710.28911070.28072373248089
1.571-1.59170.27621400.26072496263694
1.5917-1.61350.27881590.23762601276098
1.6135-1.63660.27191500.222926232773100
1.6366-1.6610.26991450.224726892834100
1.661-1.68690.25091530.21326262779100
1.6869-1.71460.27421280.205526472775100
1.7146-1.74420.24761530.211626342787100
1.7442-1.77590.27511220.211427052827100
1.7759-1.810.22441220.200726412763100
1.81-1.8470.24421200.197727372857100
1.847-1.88720.2321210.190426472768100
1.8872-1.9310.24131440.20782654279899
1.931-1.97930.2291460.188226522798100
1.9793-2.03290.23661470.18926432790100
2.0329-2.09270.24091260.190926992825100
2.0927-2.16020.20711340.192926252759100
2.1602-2.23740.23331400.19222650279099
2.2374-2.3270.2391380.19152648278698
2.327-2.43290.23481270.187926882815100
2.4329-2.56110.23551510.190126662817100
2.5611-2.72160.22921740.189126372811100
2.7216-2.93160.23731380.18112652279099
2.9316-3.22660.20791560.181226432799100
3.2266-3.69320.19911540.16772638279299
3.6932-4.6520.18281380.152699283799
4.652-41.19710.17491590.16262669282899

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