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- PDB-4rhn: HISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN (HINT) FROM RABBIT COM... -

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Basic information

Entry
Database: PDB / ID: 4rhn
TitleHISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN (HINT) FROM RABBIT COMPLEXED WITH ADENOSINE
ComponentsHISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN
KeywordsNUCLEOTIDE-BINDING PROTEIN
Function / homology
Function and homology information


purine ribonucleotide catabolic process / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / 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 / 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
alpha-D-ribofuranose / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / MIR / Resolution: 1.9 Å
AuthorsBrenner, C. / Garrison, P. / Gilmour, J. / Peisach, D. / Ringe, D. / Petsko, G.A. / Lowenstein, J.M.
CitationJournal: 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
DepositionFeb 26, 1997Processing site: BNL
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_validate_chiral / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name / _pdbx_validate_chiral.auth_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7352
Polymers12,5851
Non-polymers1501
Water1,26170
1
A: HISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN
hetero molecules

A: HISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4694
Polymers25,1692
Non-polymers3002
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area4560 Å2
ΔGint-22 kcal/mol
Surface area9650 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)50.850, 50.850, 81.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein HISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN / HINT


Mass: 12584.530 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit)
Description: RABBIT HINT CDNA WAS CLONED FROM HEART LIBRARY, EXPRESSED IN ESCHERICHIA COLI, AND PURIFIED BY ADENOSINE-AGAROSE AFFINITY CHROMATOGRAPHY
Gene: HINT / Organ: HEART / Plasmid: PSGA02-HINT / Gene (production host): HINT / Production host: Escherichia coli (E. coli) / Strain (production host): JM109/DE3/LACIQ / References: UniProt: P80912
#2: Sugar ChemComp-RIB / alpha-D-ribofuranose / alpha-D-ribose / D-ribose / ribose / Ribose


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DRibfaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-ribofuranoseCOMMON NAMEGMML 1.0
a-D-RibfIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water / 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: 2.23 Å3/Da / Density % sol: 45 %
Crystal growpH: 6.5
Details: 30% POLYETHYLENE GLYCOL 8000, 0.1 M SODIUM ACETATE,N0.1 M SODIUM CACODYLATE, PH 6.5
Crystal grow
*PLUS
Method: vapor diffusion / pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115 mg/mlprotein1drop
230 %PEG80001reservoir
30.1 Msodium acetate1reservoir
40.1 Msodium cacodylate1reservoir
50.2 mMadenosine1drop
6150 mM1dropNaCl
720 mMTris-Cl1droppH7.4

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 1, 1994 / Details: COLLIMATOR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→25.82 Å / Num. obs: 9074 / % possible obs: 84 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rsym value: 0.03 / Net I/σ(I): 10
Reflection
*PLUS
Num. measured all: 50474 / Rmerge(I) obs: 0.03

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Processing

Software
NameClassification
PROTSYSmodel building
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
XDSdata scaling
PROTSYSphasing
X-PLORphasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→10 Å / Rfactor Rfree error: 0.01 / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.264 751 8 %RANDOM
Rwork0.2 ---
obs0.2 9007 99 %-
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms878 0 10 70 958
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.74
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.43
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.9→1.99 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.438 95 11.2 %
Rwork0.382 899 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2RIB.PARWATER.TOPH
X-RAY DIFFRACTION3WATER.PARAMRIB.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.43

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