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- PDB-5o8i: Crystal structure of human histidine triad nucleotide-binding pro... -

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Basic information

Entry
Database: PDB / ID: 5o8i
TitleCrystal structure of human histidine triad nucleotide-binding protein 1 (hHINT1) crystallized at P212121 space group, and refined to 1.27 A
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
ADENOSINE-5'-DIPHOSPHATE / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 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
DepositionJun 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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)28,0753
Polymers27,6482
Non-polymers4271
Water7,458414
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-23 kcal/mol
Surface area9850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.031, 76.364, 80.864
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 12 - 125 / Label seq-ID: 12 - 125

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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
Details: First eleven amino acid residues are not visible on electron density maps
Source: (gene. exp.) Homo sapiens (human) / Gene: HINT1, HINT, PKCI1, PRKCNH1 / Plasmid: pSGA02 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P49773, Hydrolases
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.58 Å3/Da / Density % sol: 52.35 % / Description: needles
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% w/v PEG 3350, 0.1 M Bis-Tris Propane pH 8.5, 0.2 M Sodium/Potassium Phosphate

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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: 1.27→40.43 Å / Num. obs: 74711 / % possible obs: 98.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 8.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.038 / Net I/σ(I): 14.1
Reflection shellResolution: 1.27→1.29 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.535 / Num. unique obs: 3586 / CC1/2: 0.775 / Rpim(I) all: 0.461 / % possible all: 95.8

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Processing

Software
NameVersionClassification
MxCuBEdata collection
XDSdata reduction
Aimless0.5.31data scaling
MOLREP11.4.06phasing
REFMAC5.8.0158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TW2

3tw2


Resolution: 1.27→40.43 Å / Cor.coef. Fo:Fc: 0.987 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.113 / SU ML: 0.021 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.032 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13326 3746 5 %RANDOM
Rwork0.10022 ---
obs0.10183 70907 98.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.25 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0 Å20 Å2
2--0.25 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.27→40.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1789 0 27 414 2230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0192111
X-RAY DIFFRACTIONr_bond_other_d0.0020.021935
X-RAY DIFFRACTIONr_angle_refined_deg2.6521.9682898
X-RAY DIFFRACTIONr_angle_other_deg1.30834537
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0015285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.46423.97788
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.58415365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.631510
X-RAY DIFFRACTIONr_chiral_restr0.1630.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212478
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02424
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_it1.8361.1721062
X-RAY DIFFRACTIONr_mcbond_other1.8361.1721061
X-RAY DIFFRACTIONr_mcangle_it2.4731.7651373
X-RAY DIFFRACTIONr_mcangle_other2.4731.7651374
X-RAY DIFFRACTIONr_scbond_it3.8511.5841049
X-RAY DIFFRACTIONr_scbond_other3.851.5851050
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4572.2451526
X-RAY DIFFRACTIONr_long_range_B_refined4.81217.9712539
X-RAY DIFFRACTIONr_long_range_B_other4.81117.9722540
X-RAY DIFFRACTIONr_rigid_bond_restr7.01634046
X-RAY DIFFRACTIONr_sphericity_free30.6535214
X-RAY DIFFRACTIONr_sphericity_bonded11.75754169
Refine LS restraints NCS

Ens-ID: 1 / Number: 7416 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.27→1.303 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 299 -
Rwork0.185 5012 -
obs--95.85 %

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