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- PDB-1d4f: CRYSTAL STRUCTURE OF RECOMBINANT RAT-LIVER D244E MUTANT S-ADENOSY... -

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Basic information

Entry
Database: PDB / ID: 1d4f
TitleCRYSTAL STRUCTURE OF RECOMBINANT RAT-LIVER D244E MUTANT S-ADENOSYLHOMOCYSTEINE HYDROLASE
ComponentsS-ADENOSYLHOMOCYSTEINE HYDROLASE
KeywordsHYDROLASE / S-adenosylhomocysteine hydrolase / AdoHcyase / AdoHcy / Mutagenesis / X-ray crystal structure / Enzyme structure
Function / homology
Function and homology information


adenosylselenohomocysteinase activity / S-adenosylhomocysteine catabolic process / Sulfur amino acid metabolism / circadian sleep/wake cycle / adenyl nucleotide binding / chronic inflammatory response to antigenic stimulus / adenosylhomocysteinase / S-adenosylmethionine cycle / adenosylhomocysteinase activity / Methylation ...adenosylselenohomocysteinase activity / S-adenosylhomocysteine catabolic process / Sulfur amino acid metabolism / circadian sleep/wake cycle / adenyl nucleotide binding / chronic inflammatory response to antigenic stimulus / adenosylhomocysteinase / S-adenosylmethionine cycle / adenosylhomocysteinase activity / Methylation / response to nutrient / NAD binding / protein self-association / melanosome / one-carbon metabolic process / response to hypoxia / copper ion binding / endoplasmic reticulum / nucleus / identical protein binding / cytosol
Similarity search - Function
Adenosylhomocysteinase-like / Adenosylhomocysteinase-like / S-adenosyl-L-homocysteine hydrolase, conserved site / Adenosylhomocysteinase-like superfamily / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase signature 1. / S-adenosyl-L-homocysteine hydrolase signature 2. / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase, NAD binding domain ...Adenosylhomocysteinase-like / Adenosylhomocysteinase-like / S-adenosyl-L-homocysteine hydrolase, conserved site / Adenosylhomocysteinase-like superfamily / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase signature 1. / S-adenosyl-L-homocysteine hydrolase signature 2. / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Adenosylhomocysteinase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsKomoto, J. / Huang, Y. / Takusagawa, F. / Gomi, T. / Ogawa, H. / Takata, Y. / Fujioka, M.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Effects of site-directed mutagenesis on structure and function of recombinant rat liver S-adenosylhomocysteine hydrolase. Crystal structure of D244E mutant enzyme.
Authors: Komoto, J. / Huang, Y. / Gomi, T. / Ogawa, H. / Takata, Y. / Fujioka, M. / Takusagawa, F.
History
DepositionJun 22, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-ADENOSYLHOMOCYSTEINE HYDROLASE
B: S-ADENOSYLHOMOCYSTEINE HYDROLASE
C: S-ADENOSYLHOMOCYSTEINE HYDROLASE
D: S-ADENOSYLHOMOCYSTEINE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,64212
Polymers189,9194
Non-polymers3,7238
Water8,521473
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27700 Å2
ΔGint-126 kcal/mol
Surface area52510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.00, 223.00, 91.23
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-722-

HOH

21D-624-

HOH

31D-673-

HOH

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Components

#1: Protein
S-ADENOSYLHOMOCYSTEINE HYDROLASE


Mass: 47479.738 Da / Num. of mol.: 4 / Mutation: D244E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: LIVER / Production host: Escherichia coli (E. coli) / References: UniProt: P10760, adenosylhomocysteinase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-ADN / ADENOSINE / Adenosine


Mass: 267.241 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N5O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 2.44 Å3/Da / Density % sol: 49.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 22% PEG 4000, 50 mM Tris/HCl, 2% glycerol, 10% isopropanol, and 1 mM DTT. Protein concentration is 10 mg/mL., pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃ / Details: used seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 %(w/v)PEG40001reservoir
250 mMTris-HCl1reservoir
32 %(v/v)glycerol1reservoir
45 %(v/v)isopropanol1reservoir
51 mMdithiothreitol1reservoir
610 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 27, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→8 Å / Num. all: 241990 / Num. obs: 241990 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 24.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.265 / Num. unique all: 3808 / % possible all: 83.7
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 43000 / % possible obs: 85.6 % / Num. measured all: 241990 / Rmerge(I) obs: 0.093

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.8→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 4300 10 %RANDOM
Rwork0.197 ---
all0.197 43000 --
obs0.197 43000 100 %-
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13280 0 252 473 14005
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.36
X-RAY DIFFRACTIONx_dihedral_angle_d28
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 8 Å / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28

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