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- PDB-5rhn: HISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN (HINT) FROM RABBIT COM... -

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Basic information

Entry
Database: PDB / ID: 5rhn
TitleHISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN (HINT) FROM RABBIT COMPLEXED WITH 8-BR-AMP
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
8-BROMO-ADENOSINE-5'-MONOPHOSPHATE / Adenosine 5'-monophosphoramidase HINT1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / Resolution: 2.31 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 1.3Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0112
Polymers12,5851
Non-polymers4261
Water91951
1
A: HISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN
hetero molecules

A: HISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0214
Polymers25,1692
Non-polymers8522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5170 Å2
ΔGint-32 kcal/mol
Surface area9280 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)40.320, 40.320, 143.080
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: Chemical ChemComp-8BR / 8-BROMO-ADENOSINE-5'-MONOPHOSPHATE


Mass: 426.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13BrN5O7P
#3: 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: 5RHN (TETRAGONAL HINT-8-BR-AMP, ISOMORPHOUS WITH HINT WITHOUT NUCLEOTIDE) WAS DETERMINED BY REFINEMENT OF HINT WITHOUT NUCLEOTIDE.
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-IDChemical formulaDetails
115 mg/mlprotein1drop
230 %PEG80001reservoir
30.1 Msodium acetate1reservoir
40.1 Msodium cacodylate1reservoir
50.2 mM8-Br-AMP1drop
6150 mM1dropNaCl
720 mMTris-Cl1droppH7.4

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jul 1, 1996 / Details: COLLIMATOR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.31→35.13 Å / Num. obs: 5578 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 8.2 % / Rmerge(I) obs: 0.084 / Rsym value: 0.05 / Net I/σ(I): 12
Reflection shellResolution: 2.31→2.5 Å / % possible all: 97.3
Reflection
*PLUS
Num. measured all: 45935

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
R-AXISdata reduction
R-AXISdata scaling
X-PLORphasing
RefinementResolution: 2.31→10 Å / Rfactor Rfree error: 0.012 / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.264 471 8 %RANDOM
Rwork0.162 ---
obs0.162 5478 98 %-
Refinement stepCycle: LAST / Resolution: 2.31→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms878 0 24 51 953
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.71
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.46
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: 2.31→2.41 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.283 54 8.8 %
Rwork0.197 559 -
obs--97 %
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
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.46

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