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- PDB-3o1x: High resolution crystal structure of histidine triad nucleotide-b... -

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Basic information

Entry
Database: PDB / ID: 3o1x
TitleHigh resolution crystal structure of histidine triad nucleotide-binding protein 1 (Hint1) C84A mutant from rabbit complexed with adenosine
ComponentsHistidine triad nucleotide-binding protein 1
KeywordsHYDROLASE / HINT PROTEIN / HIT PROTEIN / ADENOSINE 5'-MONOPHOSPHORAMIDASE
Function / homology
Function and homology information


purine ribonucleotide catabolic process / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / intrinsic apoptotic signaling pathway by p53 class mediator / histone deacetylase complex / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / hydrolase activity / nucleotide binding ...purine ribonucleotide catabolic process / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / intrinsic apoptotic signaling pathway by p53 class mediator / histone deacetylase complex / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / hydrolase activity / nucleotide binding / regulation of DNA-templated transcription / proteolysis / nucleus / 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 / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsDolot, R.M. / Ozga, M. / Krakowiak, A.K. / Nawrot, B. / Stec, W.J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Histidine Triad Nucleotide-binding Protein 1 (HINT-1) Phosphoramidase Transforms Nucleoside 5'-O-Phosphorothioates to Nucleoside 5'-O-Phosphates.
Authors: Ozga, M. / Dolot, R. / Janicka, M. / Kaczmarek, R. / Krakowiak, A.
History
DepositionJul 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.pdbx_synchrotron_site / _software.name
Revision 1.3Sep 6, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9723
Polymers13,6821
Non-polymers2902
Water3,783210
1
A: Histidine triad nucleotide-binding protein 1
hetero molecules

A: Histidine triad nucleotide-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9446
Polymers27,3642
Non-polymers5804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area5120 Å2
ΔGint-36 kcal/mol
Surface area9770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.765, 39.765, 141.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Histidine triad nucleotide-binding protein 1 / Adenosine 5'-monophosphoramidase / P13.7


Mass: 13681.770 Da / Num. of mol.: 1 / Mutation: C84A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: HINT1, HINT / Plasmid: pSGA02 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P80912, Hydrolases
#2: Chemical ChemComp-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.04 Å3/Da / Density % sol: 39.79 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 8000, 0.1M sodium cacodylate pH 6.5, O.1M sodium acetate, protein concentration 10 mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0379 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 19, 2009 / Details: mirrors
RadiationMonochromator: Bent Si (111) crystal, horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0379 Å / Relative weight: 1
ReflectionResolution: 1.08→50 Å / Num. obs: 49845 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.15
Reflection shellResolution: 1.08→1.1 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 2.88 / Num. unique all: 2434 / % possible all: 99.7

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREP10.2.31phasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3LLJ

3llj
PDB Unreleased entry


Resolution: 1.08→23.05 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.959 / SU B: 0.815 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17139 2522 5.1 %RANDOM
Rwork0.14146 ---
all0.14296 49924 --
obs0.14296 47232 99.68 %-
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: 23.216 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.11 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.08→23.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms883 0 20 210 1113
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0211135
X-RAY DIFFRACTIONr_angle_refined_deg2.2721.9821562
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2195155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.68624.78346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56215195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.595154
X-RAY DIFFRACTIONr_chiral_restr0.1360.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021908
X-RAY DIFFRACTIONr_mcbond_it2.6641.5711
X-RAY DIFFRACTIONr_mcangle_it3.80821169
X-RAY DIFFRACTIONr_scbond_it4.8023424
X-RAY DIFFRACTIONr_scangle_it6.6844.5393
X-RAY DIFFRACTIONr_rigid_bond_restr2.58331135
LS refinement shellResolution: 1.08→1.108 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 189 -
Rwork0.303 3415 -
obs-3415 99.67 %

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