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- PDB-3o1z: High resolution crystal structure of histidine triad nucleotide-b... -

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Basic information

Entry
Database: PDB / ID: 3o1z
TitleHigh resolution crystal structure of histidine triad nucleotide-binding protein 1 (Hint1) double cysteine mutant from rabbit
ComponentsHistidine triad nucleotide-binding protein 1
KeywordsHYDROLASE / HINT PROTEIN / HIT PROTEIN / ADENOSINE 5'-MONOPHOSPHORAMIDASE
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 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases ...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 / 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 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidine triad nucleotide-binding protein 1


Theoretical massNumber of molelcules
Total (without water)13,6501
Polymers13,6501
Non-polymers00
Water4,179232
1
A: Histidine triad nucleotide-binding protein 1

A: Histidine triad nucleotide-binding protein 1


Theoretical massNumber of molelcules
Total (without water)27,2992
Polymers27,2992
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3740 Å2
ΔGint-15 kcal/mol
Surface area9820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.790, 39.790, 142.630
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: 13649.704 Da / Num. of mol.: 1 / Mutation: C38A, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.07 Å3/Da / Density % sol: 40.52 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30% PEG 8000, 0.1M sodium cacodylate pH 6.5, 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: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Sep 17, 2009 / Details: MIRRORS
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.3→26.17 Å / Num. obs: 29103 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.4 % / Biso Wilson estimate: 10.8 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 14.2
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 12.3 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 4.1 / Num. unique all: 51043 / % possible all: 99

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Processing

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

3llj
PDB Unreleased entry


Resolution: 1.3→26.17 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.664 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17612 1473 5.1 %RANDOM
Rwork0.12761 ---
all0.13002 29310 --
obs0.13002 27588 99.15 %-
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: 18.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.3→26.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms882 0 0 232 1114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0211105
X-RAY DIFFRACTIONr_angle_refined_deg2.0391.9641519
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2935156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25624.31844
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51415206
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.577155
X-RAY DIFFRACTIONr_chiral_restr0.1390.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021883
X-RAY DIFFRACTIONr_mcbond_it2.4551.5699
X-RAY DIFFRACTIONr_mcangle_it3.55121153
X-RAY DIFFRACTIONr_scbond_it4.9113406
X-RAY DIFFRACTIONr_scangle_it6.8064.5366
X-RAY DIFFRACTIONr_rigid_bond_restr1.54511105
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 102 -
Rwork0.204 1999 -
obs-1999 98.18 %

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