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- PDB-1rzy: Crystal structure of rabbit Hint complexed with N-ethylsulfamoyla... -

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Basic information

Entry
Database: PDB / ID: 1rzy
TitleCrystal structure of rabbit Hint complexed with N-ethylsulfamoyladenosine
ComponentsHistidine triad nucleotide-binding protein 1
KeywordsHYDROLASE / HIT protein / protein-inhibitor complex
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
5'-O-(N-ETHYL-SULFAMOYL)ADENOSINE / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsKrakowiak, A.K. / Pace, H.C. / Blackburn, G.M. / Adams, M. / Mekhalfia, A. / Kaczmarek, R. / Baraniak, J. / Stec, W.J. / Brenner, C.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Biochemical, crystallographic, and mutagenic characterization of hint, the AMP-lysine hydrolase, with novel substrates and inhibitors
Authors: Krakowiak, A.K. / Pace, H.C. / Blackburn, G.M. / Adams, M. / Mekhalfia, A. / Kaczmarek, R. / Baraniak, J. / Stec, W.J. / Brenner, C.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: Crystal structures of HINT demonstrate that histidine triad proteins are GalT-related nucleotide-binding proteins
Authors: Brenner, C. / Garrison, P. / Gilmour, J. / Peisach, D. / Ringe, D. / Petsko, G.A. / Lowenstein, J.M.
History
DepositionDec 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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)14,0882
Polymers13,7141
Non-polymers3741
Water1,26170
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)28,1764
Polymers27,4282
Non-polymers7492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5180 Å2
ΔGint-17 kcal/mol
Surface area9230 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)39.888, 39.888, 142.286
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212

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Components

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


Mass: 13713.835 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: HINT1, HINT / Organ: heart / Production host: Escherichia coli (E. coli) / References: UniProt: P80912
#2: Chemical ChemComp-5AS / 5'-O-(N-ETHYL-SULFAMOYL)ADENOSINE


Mass: 374.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18N6O6S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.1 Å3/Da / Density % sol: 41.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.4
Details: sodium acetate, cacodylate, PEG8000, pH 7.4, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion / Details: Brenner, C., (1997) Nat.Struct.Biol., 4, 231.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
230 %PEG80001reservoir
30.1 Msodium acetate1reservoir
40.1 Msodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 26, 2002 / Details: osmic confocal blue
RadiationMonochromator: Osmic Confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→23 Å / Num. obs: 10698 / % possible obs: 93.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 8.4 % / Biso Wilson estimate: 16.9 Å2 / Rsym value: 0.0065 / Net I/σ(I): 9.2
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 5.1 / Num. unique all: 968 / Rsym value: 0.143 / % possible all: 88.3
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 23 Å / Num. measured all: 95355 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 88.3 % / Rmerge(I) obs: 0.143

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Processing

Software
NameVersionClassification
crystalcleardata collection
d*TREKdata reduction
CNSrefinement
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→23 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 773 7.8 %RANDOM
Rwork0.216 ---
all0.217 10698 --
obs0.217 9925 --
Refinement stepCycle: LAST / Resolution: 1.8→23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms866 0 25 70 961
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.416
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_improper_angle_d0.854
X-RAY DIFFRACTIONc_dihedral_angle_d23.523
X-RAY DIFFRACTIONc_mcbond_it1.0161.5
X-RAY DIFFRACTIONc_scbond_it1.8082
X-RAY DIFFRACTIONc_mcangle_it1.4342
X-RAY DIFFRACTIONc_scangle_it2.5342.5
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 23 Å / % reflection Rfree: 7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.523
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.854
LS refinement shell
*PLUS
Rfactor Rfree: 0.281 / Rfactor Rwork: 0.299

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