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- PDB-3dhy: Crystal Structures of Mycobacterium tuberculosis S-Adenosyl-L-Hom... -

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Basic information

Entry
Database: PDB / ID: 3dhy
TitleCrystal Structures of Mycobacterium tuberculosis S-Adenosyl-L-Homocysteine Hydrolase in Ternary Complex with Substrate and Inhibitors
ComponentsAdenosylhomocysteinase
KeywordsHYDROLASE / Protein-substrate complex / dimer of dimers / NAD binding domain / 37 amino acid insertion / solvent access channel / Structural Genomics / Tuberculosis structural genomics Consortium / TB Structural Genomics Consortium / TBSGC / Cytoplasm / NAD / One-carbon metabolism / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


adenosylhomocysteinase / L-methionine catabolic process / entry of bacterium into host cell / adhesion of symbiont to host cell / adenosine metabolic process / L-homocysteine biosynthetic process / adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / zymogen binding ...adenosylhomocysteinase / L-methionine catabolic process / entry of bacterium into host cell / adhesion of symbiont to host cell / adenosine metabolic process / L-homocysteine biosynthetic process / adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / zymogen binding / NAD+ binding / one-carbon metabolic process / peptidoglycan-based cell wall / extracellular region / plasma membrane / cytoplasm / 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
5'-S-ethyl-5'-thioadenosine / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Adenosylhomocysteinase / Adenosylhomocysteinase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShetty, N.D. / Ioerger, T.R. / Gokulan, K. / Reddy, M.C.M. / Owen, J.L. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Protein Sci. / Year: 2008
Title: Crystal structures of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with substrate and inhibitors.
Authors: Reddy, M.C. / Kuppan, G. / Shetty, N.D. / Owen, J.L. / Ioerger, T.R. / Sacchettini, J.C.
History
DepositionJun 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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

Downloads & links

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Assembly

Deposited unit
A: Adenosylhomocysteinase
B: Adenosylhomocysteinase
C: Adenosylhomocysteinase
D: Adenosylhomocysteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,44912
Polymers217,5504
Non-polymers3,8998
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26900 Å2
ΔGint-122 kcal/mol
Surface area62080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.200, 111.690, 100.130
Angle α, β, γ (deg.)90.00, 96.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Adenosylhomocysteinase / S-adenosyl-L-homocysteine hydrolase / AdoHcyase


Mass: 54387.410 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: ahcY, sahH, Rv3248c, MT3346, MTCY20B11.23c / Plasmid: pET28TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P60176, UniProt: P9WGV3*PLUS, adenosylhomocysteinase
#2: Chemical
ChemComp-3DH / 5'-S-ethyl-5'-thioadenosine / S-adenosylethane


Mass: 311.360 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H17N5O3S
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.41 Å3/Da / Density % sol: 48.92 %
Crystal growTemperature: 291.5 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M MgCl2, 0.1 M Tris pH 8.5, 25% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 16, 2008 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.2→99.5 Å / Num. obs: 384395 / % possible obs: 58.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.309 / Net I/σ(I): 2
Reflection shellResolution: 1.19→1.23 Å / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 0.7 / % possible all: 3.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
d*TREKdata reduction
d*TREKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CE6

3ce6


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.883 / SU B: 7.529 / SU ML: 0.209 / Cross valid method: THROUGHOUT / ESU R: 0.327 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.34004 5714 5 %RANDOM
Rwork0.26007 ---
obs0.26405 108886 82.51 %-
all-114623 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.22 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å20 Å20.75 Å2
2--1.87 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14998 0 260 350 15608
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02215586
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.97721184
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.51451937
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.43924.798692
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.45152601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8521584
X-RAY DIFFRACTIONr_chiral_restr0.1040.22369
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211752
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2180.27106
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.210526
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2556
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.229
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.96159868
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.006715444
X-RAY DIFFRACTIONr_scbond_it6.90396544
X-RAY DIFFRACTIONr_scangle_it8.206115740
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 441 -
Rwork0.301 8634 -
obs--89.29 %

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