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- PDB-6rhn: HISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN (HINT) FROM RABBIT WIT... -

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Basic information

Entry
Database: PDB / ID: 6rhn
TitleHISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN (HINT) FROM RABBIT WITHOUT NUCLEOTIDE
ComponentsHISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN
KeywordsNUCLEOTIDE-BINDING PROTEIN
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 / MOLECULAR REPLACEMENT / Resolution: 2.15 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 27, 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 1.3Aug 9, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)12,5851
Polymers12,5851
Non-polymers00
Water91951
1
A: HISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN

A: HISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)25,1692
Polymers25,1692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3810 Å2
ΔGint-16 kcal/mol
Surface area9540 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)40.340, 40.340, 143.030
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 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.08 Å3/Da / Density % sol: 41 %
Description: 6RHN (TETRAGONAL HINT WITHOUT NUCLEOTIDE) WAS DETERMINED BY MR WITH HINT COORDINATES FROM HINT-ADENOSINE.
Crystal growpH: 6.5
Details: 30% POLYETHYLENE GLYCOL 8000, 0.1 M SODIUM ACETATE, 0.1 M SODIUM CACODYLATE, PH 6.5
Crystal grow
*PLUS
Method: vapor diffusion / pH: 7.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
230 %PEG80001reservoir
30.1 Msodium acetate1reservoir
40.1 Msodium cacodylate1reservoir
520 mMTris-Cl1drop
6150 mM1droppH7.4NaCl

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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: Feb 1, 1995 / Details: COLLIMATOR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→35.14 Å / Num. obs: 6302 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.046
Reflection shellResolution: 2.15→2.27 Å / % possible all: 59
Reflection
*PLUS
Num. measured all: 42366

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
XDSdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PROTEIN PORTION OF HINT-ADENOSINE MODEL, PDB ENTRY 4RHN

4rhn


Resolution: 2.15→10 Å / Rfactor Rfree error: 0.012 / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.263 503 8 %RANDOM
Rwork0.176 ---
obs0.176 6205 91 %-
Refinement stepCycle: LAST / Resolution: 2.15→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms878 0 0 51 929
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_deg1.62
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.41
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: 2.15→2.25 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.232 47 9.7 %
Rwork0.234 437 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2WATER.PARAMWATER.TOPH
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.41

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