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- PDB-6g9z: Crystal structure of human histidine triad nucleotide-binding pro... -

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Basic information

Entry
Database: PDB / ID: 6g9z
TitleCrystal structure of human histidine triad nucleotide-binding protein 1 (hHINT1) crystallized at P212121 space group, with visible extended fragment of N-terminus
ComponentsHistidine triad nucleotide-binding protein 1
KeywordsHYDROLASE / phosphoramidase / desulfurase / tumour suppressor
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 / 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
(2S)-2-hydroxybutanedioic acid / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsDolot, R.M. / Seda, A. / Nawrot, B.C.
CitationJournal: To Be Published
Title: Differences in crystal packing as the key factor for stabilization of the N-terminal fragment of hHINT1 protein
Authors: Dolot, R.M. / Seda, A. / Nawrot, B.C.
History
DepositionApr 11, 2018Deposition site: PDBE / Processing site: PDBE
SupersessionApr 18, 2018ID: 5O8G
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
A: Histidine triad nucleotide-binding protein 1
B: Histidine triad nucleotide-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7823
Polymers27,6482
Non-polymers1341
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-17 kcal/mol
Surface area11380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.075, 63.379, 76.836
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 BL21 (bacteria) / References: UniProt: P49773, Hydrolases
#2: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 2.55 Å3/Da / Density % sol: 51.72 %
Description: Plates of typical dimensions 0.6 x 0.35 x 0.05 mm
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 25% PEG 1500, 0.1 M MMT Buffer pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2016
RadiationMonochromator: Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.43→39.52 Å / Num. obs: 40954 / % possible obs: 96.1 % / Redundancy: 3.77 % / Biso Wilson estimate: 15 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.137 / Rrim(I) all: 0.161 / Net I/σ(I): 8.78
Reflection shellResolution: 1.43→1.51 Å / Redundancy: 3.74 % / Rmerge(I) obs: 0.703 / Mean I/σ(I) obs: 1.96 / Num. unique obs: 6294 / CC1/2: 0.833 / Rrim(I) all: 0.821 / % possible all: 92.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TW2

3tw2


Resolution: 1.43→39.52 Å / Cor.coef. Fo:Fc: 0.857 / Cor.coef. Fo:Fc free: 0.828 / SU B: 4.23 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.102 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27726 2041 5 %RANDOM
Rwork0.22362 ---
obs0.2263 38759 95.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 9.995 Å2
Baniso -1Baniso -2Baniso -3
1--0.73 Å2-0 Å2-0 Å2
2--0.29 Å2-0 Å2
3---0.44 Å2
Refinement stepCycle: 1 / Resolution: 1.43→39.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1841 0 9 401 2251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0152069
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171890
X-RAY DIFFRACTIONr_angle_refined_deg1.8121.7472817
X-RAY DIFFRACTIONr_angle_other_deg0.611.7214460
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6765276
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44219.06264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.0915321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4121510
X-RAY DIFFRACTIONr_chiral_restr0.0960.2260
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212422
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02370
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1180.7251053
X-RAY DIFFRACTIONr_mcbond_other2.1170.7241054
X-RAY DIFFRACTIONr_mcangle_it2.3231.0891346
X-RAY DIFFRACTIONr_mcangle_other2.3231.0891346
X-RAY DIFFRACTIONr_scbond_it1.9270.9051016
X-RAY DIFFRACTIONr_scbond_other1.9280.9031013
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5591.2791470
X-RAY DIFFRACTIONr_long_range_B_refined4.38811.5382395
X-RAY DIFFRACTIONr_long_range_B_other3.69810.1142267
X-RAY DIFFRACTIONr_rigid_bond_restr3.45733959
X-RAY DIFFRACTIONr_sphericity_free30.8015213
X-RAY DIFFRACTIONr_sphericity_bonded12.11354085
LS refinement shellResolution: 1.427→1.464 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.477 146 -
Rwork0.419 2778 -
obs--94.69 %

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