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- PDB-3tw2: High resolution structure of human histidine triad nucleotide-bin... -

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Basic information

Entry
Database: PDB / ID: 3tw2
TitleHigh resolution structure of human histidine triad nucleotide-binding protein 1 (hHINT1)/AMP complex in a monoclinic space group
ComponentsHistidine triad nucleotide-binding protein 1
KeywordsHYDROLASE
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 / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of calcium-mediated signaling ...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 / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / Transcriptional and post-translational regulation of MITF-M expression and activity / 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
ADENOSINE MONOPHOSPHATE / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsDolot, R.M. / Wlodarczyk, A. / Ozga, M. / Krakowiak, A. / Nawrot, B.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: A new crystal form of human histidine triad nucleotide-binding protein 1 (hHINT1) in complex with adenosine 5'-monophosphate at 1.38 A resolution.
Authors: Dolot, R. / Ozga, M. / Wlodarczyk, A. / Krakowiak, A. / Nawrot, B.
History
DepositionSep 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Database references
Revision 1.2Jan 23, 2013Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)27,9953
Polymers27,6482
Non-polymers3471
Water7,368409
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-26 kcal/mol
Surface area9660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.421, 46.449, 64.034
Angle α, β, γ (deg.)90.00, 94.42, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-364-

HOH

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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: 13823.931 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HINT1, HINT, PKCI1, PRKCNH1 / Plasmid: pSGA02 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P49773, Hydrolases
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.08 Å3/Da / Density % sol: 40.75 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 19% PEG 8000, 0.1M sodium cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 8, 2011
RadiationMonochromator: Bent Si (111) crystal, horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 1.38→25.58 Å / Num. all: 45932 / Num. obs: 45932 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 13.1
Reflection shellResolution: 1.38→1.45 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.291 / Mean I/σ(I) obs: 3.4 / Num. unique all: 5760 / % possible all: 84

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KPF

1kpf


Resolution: 1.38→25.58 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.965 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16148 2320 5.1 %RANDOM
Rwork0.12073 ---
all0.12277 46364 --
obs0.12277 43580 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.709 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20 Å2-0.02 Å2
2---0.76 Å20 Å2
3----0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.38→25.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1767 0 23 409 2199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212148
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.9772950
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7935293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.03524.25387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.0515385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1961510
X-RAY DIFFRACTIONr_chiral_restr0.1040.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211701
X-RAY DIFFRACTIONr_mcbond_it1.2191.51343
X-RAY DIFFRACTIONr_mcangle_it1.90622214
X-RAY DIFFRACTIONr_scbond_it3.0273805
X-RAY DIFFRACTIONr_scangle_it4.2084.5736
X-RAY DIFFRACTIONr_rigid_bond_restr1.4432148
LS refinement shellResolution: 1.384→1.42 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 150 -
Rwork0.198 2918 -
obs--89.52 %

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