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- PDB-1li4: Human S-adenosylhomocysteine hydrolase complexed with neplanocin -

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Basic information

Entry
Database: PDB / ID: 1li4
TitleHuman S-adenosylhomocysteine hydrolase complexed with neplanocin
ComponentsS-adenosylhomocysteine hydrolase
KeywordsHYDROLASE / alpha-beta structure / inhibitor complex
Function / homology
Function and homology information


Defective AHCY causes HMAHCHD / Sulfur amino acid metabolism / Metabolism of ingested SeMet, Sec, MeSec into H2Se / adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / Methylation / melanosome / one-carbon metabolic process / endoplasmic reticulum ...Defective AHCY causes HMAHCHD / Sulfur amino acid metabolism / Metabolism of ingested SeMet, Sec, MeSec into H2Se / adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / Methylation / melanosome / one-carbon metabolic process / endoplasmic reticulum / extracellular exosome / 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
ISOPROPYL ALCOHOL / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-NOC / Adenosylhomocysteinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsYang, X. / Hu, Y. / Yin, D.H. / Turner, M.A. / Wang, M. / Borchardt, R.T. / Howell, P.L. / Kuczera, K. / Schowen, R.L.
CitationJournal: Biochemistry / Year: 2003
Title: Catalytic strategy of S-adenosyl-L-homocysteine hydrolase: Transition-state stabilization and the avoidance of abortive reactions
Authors: Yang, X. / Hu, Y. / Yin, D.H. / Turner, M.A. / Wang, M. / Borchardt, R.T. / Howell, P.L. / Kuczera, K. / Schowen, R.L.
History
DepositionApr 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: S-adenosylhomocysteine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8225
Polymers47,7731
Non-polymers1,0494
Water3,837213
1
A: S-adenosylhomocysteine hydrolase
hetero molecules

A: S-adenosylhomocysteine hydrolase
hetero molecules

A: S-adenosylhomocysteine hydrolase
hetero molecules

A: S-adenosylhomocysteine hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,28720
Polymers191,0924
Non-polymers4,19616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area30420 Å2
ΔGint-108 kcal/mol
Surface area50450 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.830, 135.670, 171.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Detailsbiological unit is a tetramer which can be generated using the crystallographic symmetry operators: -X, -Y, Z; -X, Y, -Z; X, -Y, -Z

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Components

#1: Protein S-adenosylhomocysteine hydrolase


Mass: 47772.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pPROKcd20 / Production host: Escherichia coli (E. coli) / References: UniProt: P23526, adenosylhomocysteinase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-NOC / 3-(6-AMINO-PURIN-9-YL)-5-HYDROXYMETHYL-CYCLOPENTANE-1,2-DIOL / NEPLANOCIN


Mass: 265.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N5O3
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.82 Å3/Da / Density % sol: 56.45 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG4K, IOSPROPANOL, AMMONIUM ACETATE, CITRATE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
128 mg/mlprotein1drop
212 %(w/v)PEG40001reservoir
320 %(v/v)2-propanol1reservoir
4200 mMammonium acetate1reservoir
5100 mMcitrate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1998
RadiationMonochromator: Collimating mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. all: 35337 / Num. obs: 35337 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 18.5
Reflection shellResolution: 2.01→2.08 Å / Rmerge(I) obs: 0.268 / % possible all: 91.4
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 201201
Reflection shell
*PLUS
% possible obs: 91.4 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1A7A

1a7a


Resolution: 2.01→29.71 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 814101.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 3434 10 %RANDOM
Rwork0.197 ---
all0.197 35337 --
obs0.197 34435 95 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.9451 Å2 / ksol: 0.397558 e/Å3
Displacement parametersBiso mean: 28.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.44 Å20 Å20 Å2
2---5.68 Å20 Å2
3---1.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.01→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 71 213 3606
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d1.23
LS refinement shellResolution: 2.01→2.13 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.291 491 10.1 %
Rwork0.247 4372 -
obs--80.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMNOV19NAHNEP.TOP
X-RAY DIFFRACTION3NOV19NAHNEP.PAR
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.23

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