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- PDB-1b3r: RAT LIVER S-ADENOSYLHOMOCYSTEIN HYDROLASE -

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Basic information

Entry
Database: PDB / ID: 1b3r
TitleRAT LIVER S-ADENOSYLHOMOCYSTEIN HYDROLASE
ComponentsPROTEIN (S-ADENOSYLHOMOCYSTEINE HYDROLASE)
KeywordsHYDROLASE / ADEONSYLHOMOCYSTEINE / ADOHCY / ADOHCYASE
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 / : / melanosome / one-carbon metabolic process / response to hypoxia / copper ion binding / endoplasmic reticulum / identical protein binding / nucleus / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Adenosylhomocysteinase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHu, Y. / Komoto, J. / Huang, Y. / Takusagawa, F. / Gomi, T. / Ogawa, H. / Takata, Y. / Fujioka, M.
CitationJournal: Biochemistry / Year: 1999
Title: Crystal structure of S-adenosylhomocysteine hydrolase from rat liver.
Authors: Hu, Y. / Komoto, J. / Huang, Y. / Gomi, T. / Ogawa, H. / Takata, Y. / Fujioka, M. / Takusagawa, F.
History
DepositionDec 14, 1998Processing site: RCSB
Revision 1.0Dec 23, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)192,5178
Polymers189,8634
Non-polymers2,6544
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23710 Å2
ΔGint-106 kcal/mol
Surface area56490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.760, 134.480, 102.260
Angle α, β, γ (deg.)90.00, 114.35, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.999862, 0.014624, 0.007919), (-0.013128, -0.986364, 0.164057), (0.01021, 0.16393, 0.986419)47.2466, 0.4231, -0.2142
2given(-0.999882, 0.015133, -0.002566), (-0.014478, 0.985377, -0.169771), (0.005097, -0.169714, 0.98548)47.2856, 0.2216, -0.0268
3given(0.999979, 0.003426, -0.005466), (0.00341, -0.99999, -0.00282), (-0.005476, 0.002802, -0.999981)0.0135, 0.0856, 0.1867

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Components

#1: Protein
PROTEIN (S-ADENOSYLHOMOCYSTEINE HYDROLASE)


Mass: 47465.711 Da / Num. of mol.: 4 / Fragment: CATALYTIC DOMAIN (1 - 181 & 352 - 402)
Source method: isolated from a genetically manipulated source
Details: EACH SUBUNIT CONTAINS ONE NAD+ MOLECULE. / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Strain: MV1304 / Organ: LIVER / Plasmid: PUC118 / Production host: Escherichia coli (E. coli) / Strain (production host): MV1304 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60 %
Crystal growpH: 6.8
Details: 50 MM TRIS/HCL (PH 6.8), 6 MM MGCL2, 5% MPD, 15% PEG-6K
Components of the solutions
IDNameCrystal-IDSol-ID
150 MM TRIS/HCL (PH 6.8)12
26 MM MGCL212
315% PEG-6K12
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 26 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMTris-HCl1drop
210 mM1dropMgCl2
315 %(w/v)PEG60001drop
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 56314 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 10.1
Reflection shellResolution: 2.8→3 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.173 / % possible all: 98
Reflection
*PLUS
Num. measured all: 280288 / Rmerge(I) obs: 0.07

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
DENZOdata reduction
KUMDSdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NAD-BINDING DOMAIN IN FORMATE DEHYDROGENASE

Resolution: 2.8→8 Å / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: APPLIED / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.269 -5 %RANDOM SELECTION
Rwork0.199 ---
obs-56314 97.5 %-
Displacement parametersBiso mean: 21.5 Å2
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16088 0 208 1239 17535
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_d24.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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: 2.8→2.92 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.362 -5 %
Rwork0.273 5843 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN-REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.NADTOPOLOGY.NAD
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 8 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.362 / % reflection Rfree: 5 % / Rfactor Rwork: 0.273

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