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- PDB-4g89: Crystal structure of k. pneumoniae mta/adohcy nucleosidase in com... -

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Basic information

Entry
Database: PDB / ID: 4g89
TitleCrystal structure of k. pneumoniae mta/adohcy nucleosidase in complex with fragmented s-adenosyl-l-homocysteine
Components5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
KeywordsHYDROLASE / MIXED ALPHA/BETA / DIMER / S-ADENOSYLHOMOCYSTEINE / CLEAVAGE
Function / homology
Function and homology information


purine deoxyribonucleoside catabolic process / L-methionine salvage from S-adenosylmethionine / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / L-methionine salvage from methylthioadenosine / cytoplasm
Similarity search - Function
MTA/SAH nucleosidase / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENINE / S-ADENOSYL-L-HOMOCYSTEINE / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNorris, G.E. / Brown, R.L. / Anderson, B.F. / Tyler, P.C. / Evans, G.B.
CitationJournal: To be Published
Title: Crystal structure of k. pneumoniae mta/adohcy nucleosidase in complex with fragmented s-adenosyl-l-homocysteine
Authors: Norris, G.E. / Brown, R.L. / Anderson, B.F. / Tyler, P.C. / Evans, G.B.
History
DepositionJul 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
B: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6495
Polymers50,0332
Non-polymers6163
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-31 kcal/mol
Surface area18040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.346, 59.242, 82.926
Angle α, β, γ (deg.)90.00, 128.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase / MTA/SAH nucleosidase / MTAN / 5'-methylthioadenosine nucleosidase / MTA nucleosidase / S- ...MTA/SAH nucleosidase / MTAN / 5'-methylthioadenosine nucleosidase / MTA nucleosidase / S-adenosylhomocysteine nucleosidase / AdoHcy nucleosidase / SAH nucleosidase / SRH nucleosidase


Mass: 25016.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Strain: MGH 78578 ATCC 70072 / Gene: KPN 00174, KPN78578_01730, KPN_00174, mtnN / Plasmid: pPROEX HTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: A6T4W3, adenosylhomocysteine nucleosidase
#2: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.07 Å3/Da / Density % sol: 40.66 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.67M AMMONIUM SULPHATE, 80MM HEPES PH 7.5, 1.7% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 3, 2006 / Details: CAPILLIARY
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2x-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30.64 Å / Num. all: 25670 / Num. obs: 25670 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 24.34 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 13.6
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1671 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: S.AUREUS MTAN

Resolution: 2.1→30.64 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.935 / SU B: 5.606 / SU ML: 0.145 / Isotropic thermal model: ISOTROPIC WITH TLS / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.186 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21982 1294 5 %RANDOM
Rwork0.16005 ---
all0.16307 25670 --
obs0.16307 24376 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.615 Å2
Baniso -1Baniso -2Baniso -3
1-4.7 Å20 Å22.89 Å2
2---1.86 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3450 0 31 278 3759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193598
X-RAY DIFFRACTIONr_bond_other_d0.0010.022335
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.9644883
X-RAY DIFFRACTIONr_angle_other_deg1.08835745
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.5545481
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.56924.861144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.56715605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9741519
X-RAY DIFFRACTIONr_chiral_restr0.1060.2581
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024104
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02689
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 82 -
Rwork0.263 1671 -
obs-1671 96.27 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
113.6975-2.4478-3.2333.8269-2.71193.96790.28041.2745-0.4334-0.2211-0.06350.43850.063-0.517-0.21690.12680.1787-0.10950.383-0.13410.24215.779-3.4323.689
273.0543-32.13725.484415.8495-9.096926.51333.13144.7909-8.2726-1.1365-2.13143.7529-0.67480.6521-10.453-0.1224-0.53720.7761-0.29951.090618.468-3.724-8.366
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B153 - 169
2X-RAY DIFFRACTION2B197 - 209

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