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- PDB-4qez: Crystal structure of 5'-methylthioadenosine/S-adenosylhomocystein... -

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Basic information

Entry
Database: PDB / ID: 4qez
TitleCrystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Bacillus anthracis
Components5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
KeywordsHYDROLASE / Amino-acid biosynthesis / Methionine biosynthesis
Function / homology
Function and homology information


adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / L-methionine salvage from S-adenosylmethionine / nucleoside catabolic process / L-methionine salvage from methylthioadenosine / cytosol
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 / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTarique, K.F. / Devi, S. / Abdul Rehman, S.A. / Gourinath, S.
CitationJournal: To be Published
Title: Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Bacillus anthracis
Authors: Tarique, K.F. / Devi, S. / Abdul Rehman, S.A. / Gourinath, S.
History
DepositionMay 19, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.2Nov 8, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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
B: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
A: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
C: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,8349
Polymers79,0623
Non-polymers7726
Water00
1
B: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
A: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2236
Polymers52,7082
Non-polymers5154
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-1 kcal/mol
Surface area17340 Å2
MethodPISA
2
C: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules

C: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2236
Polymers52,7082
Non-polymers5154
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area4210 Å2
ΔGint-1 kcal/mol
Surface area18220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.269, 74.635, 46.688
Angle α, β, γ (deg.)90.00, 95.26, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12B
22C
13A
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUBA2 - 2292 - 229
21GLUGLUAB2 - 2292 - 229
12HISHISBA2 - 2372 - 237
22HISHISCC2 - 2372 - 237
13GLUGLUAB2 - 2292 - 229
23GLUGLUCC2 - 2292 - 229

NCS ensembles :
ID
1
2
3

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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: 26353.990 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: sterne / Gene: mtnN, BA_4602, GBAA_4602, BAS4270 / Plasmid: pET28(B) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q81LL4, adenosylhomocysteine nucleosidase
#2: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H5N5
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM

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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: 1.99 Å3/Da / Density % sol: 38.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2M Ammonium sulfate, 0.2M MgCl2, Tris pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 16291 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rsym value: 0.08 / Net I/σ(I): 21.64
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.549 / Rsym value: 0.34 / % possible all: 75

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DP9

3dp9


Resolution: 2.7→34.49 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.895 / SU B: 40.202 / SU ML: 0.362 / Cross valid method: THROUGHOUT / ESU R Free: 0.446 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27145 819 5 %RANDOM
Rwork0.24104 ---
obs0.24258 15438 94.89 %-
all-23990 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.04 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å20 Å2-0.6 Å2
2---1.95 Å2-0 Å2
3---1.03 Å2
Refine analyzeLuzzati coordinate error obs: 0.475 Å
Refinement stepCycle: LAST / Resolution: 2.7→34.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5265 0 54 0 5319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195405
X-RAY DIFFRACTIONr_bond_other_d0.0030.025222
X-RAY DIFFRACTIONr_angle_refined_deg1.1761.9597301
X-RAY DIFFRACTIONr_angle_other_deg1.048311995
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1475679
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79625.041246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.52815931
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2021524
X-RAY DIFFRACTIONr_chiral_restr0.0730.2837
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026123
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021204
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8935.5442734
X-RAY DIFFRACTIONr_mcbond_other0.8935.5442733
X-RAY DIFFRACTIONr_mcangle_it1.6138.3133407
X-RAY DIFFRACTIONr_mcangle_other1.6138.3133408
X-RAY DIFFRACTIONr_scbond_it0.5625.6672568
X-RAY DIFFRACTIONr_scbond_other0.5625.6672569
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0938.4653767
X-RAY DIFFRACTIONr_long_range_B_refined2.63443.1195735
X-RAY DIFFRACTIONr_long_range_B_other2.63443.1195735
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11B13212
12A13212
21B13567
22C13567
31A13228
32C13228
LS refinement shellResolution: 2.705→2.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 40 -
Rwork0.32 847 -
obs--69.73 %
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)
12.8701-0.97890.70512.42840.1692.9467-0.05830.0625-0.05250.1449-0.0148-0.26330.14520.27190.07310.0184-0.0137-0.00880.2773-0.02850.101742.478-22.66110.741
22.2052-1.04580.53091.80680.3742.7533-0.1373-0.14520.1259-0.0183-0.01060.0767-0.2503-1.00670.1480.02980.085-0.03350.6377-0.08710.103216.059-11.37610.205
32.73280.51941.86291.62220.34484.05760.0702-0.0537-0.02980.1113-0.0477-0.18950.2510.287-0.02250.15640.0173-0.00610.3634-0.00780.213413.12-49.039-13.432
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B2 - 237
2X-RAY DIFFRACTION2A2 - 230
3X-RAY DIFFRACTION3C2 - 237

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