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- PDB-6po4: 2.1 Angstrom Resolution Crystal Structure of 5'-methylthioadenosi... -

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Entry
Database: PDB / ID: 6po4
Title2.1 Angstrom Resolution Crystal Structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (mtnN) from Haemophilus influenzae PittII.
Components5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
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
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 / BORIC ACID / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
Similarity search - Component
Biological speciesHaemophilus influenzae PittII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMinasov, G. / Shuvalova, L. / Cardona-Correa, A. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 2.1 Angstrom Resolution Crystal Structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase (mtnN) from Haemophilus influenzae PittII.
Authors: Minasov, G. / Shuvalova, L. / Cardona-Correa, A. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJul 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Apr 3, 2024Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms

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


Theoretical massNumber of molelcules
Total (without water)149,55824
Polymers147,5656
Non-polymers1,99318
Water13,709761
1
A: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
B: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8538
Polymers49,1882
Non-polymers6646
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-19 kcal/mol
Surface area17360 Å2
MethodPISA
2
C: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
D: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8538
Polymers49,1882
Non-polymers6646
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-13 kcal/mol
Surface area17280 Å2
MethodPISA
3
E: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
F: 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8538
Polymers49,1882
Non-polymers6646
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-17 kcal/mol
Surface area17180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.536, 214.743, 146.904
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-406-

HOH

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Components

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


Mass: 24594.146 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae PittII (bacteria)
Gene: mtnN, CGSHiII_00894 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Magic
References: UniProt: A0A0E1SMD9, adenosylhomocysteine nucleosidase
#2: Chemical
ChemComp-HCS / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / L-Homocysteine


Type: L-peptide linking / Mass: 135.185 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H9NO2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H5N5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: BH3O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 761 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.35 Å3/Da / Density % sol: 63.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Protein: 14.5 mg/ml, 0.01M Tris pH 8.3; Screen: Classics II (B5), 1.26M Sodium phosphate, 0.14M Potassium phosphate; Cryo: 1:1, reservoir : 50% Sucrose.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 12, 2017 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 115902 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 38.7 Å2 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.035 / Rrim(I) all: 0.089 / Rsym value: 0.081 / Χ2: 1.005 / Net I/σ(I): 19.8
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 5754 / CC1/2: 0.807 / Rpim(I) all: 0.318 / Rrim(I) all: 0.806 / Rsym value: 0.74 / Χ2: 1.01 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3o4v

3o4v


Resolution: 2.1→29.87 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 7.112 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.131
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1907 5621 4.9 %RANDOM
Rwork0.1603 ---
obs0.1618 108746 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 127.68 Å2 / Biso mean: 44.826 Å2 / Biso min: 17.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å20 Å2
2---2.38 Å20 Å2
3---3.18 Å2
Refinement stepCycle: final / Resolution: 2.1→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10256 0 32 784 11072
Biso mean--62.19 48.66 -
Num. residues----1405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01310513
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710164
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.62614165
X-RAY DIFFRACTIONr_angle_other_deg0.3251.5823592
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.11651392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.62324.943439
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.014151866
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1981536
X-RAY DIFFRACTIONr_chiral_restr0.0550.21446
X-RAY DIFFRACTIONr_gen_planes_refined0.0570.0211906
X-RAY DIFFRACTIONr_gen_planes_other0.0560.021920
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 376 -
Rwork0.231 7969 -
all-8345 -
obs--100 %
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)
11.18521.32741.55283.90660.01424.2084-0.127100.0454-0.08730.13630.43930.106-0.2967-0.00920.1536-0.06790.01470.33380.04580.198926.1161-37.5339-0.3156
21.4380.68890.52152.03280.16961.5378-0.0071-0.21550.08930.36450.05560.4572-0.0136-0.4363-0.04850.1160.05810.09010.27010.04490.109328.079-32.490116.0229
35.756-3.57853.86127.9548-3.07084.1850.21070.00680.11690.0312-0.1840.5220.2864-0.3212-0.02680.0303-0.03690.02060.20290.06070.107819.7993-41.73399.2747
40.75080.77790.01274.071-1.20923.06960.03270.0140.044-0.00660.0796-0.1645-0.4609-0.021-0.11230.19110.0045-0.02130.07080.00920.0748.6656-9.34063.9768
50.5681-0.0819-0.06172.39970.11180.9524-0.0697-0.03790.04010.27580.0252-0.3091-0.13740.1090.04450.1350.0159-0.06930.13020.0040.052252.8853-22.578413.841
61.5969-1.8562-2.84363.0791.69411.40730.1248-0.02450.28650.0525-0.0379-0.4284-0.18840.4221-0.08690.1292-0.0364-0.00640.10550.02640.13361.1719-11.65886.0278
71.55-0.58380.79744.76021.84842.7650.1087-0.0771-0.3121-0.2915-0.0850.29570.3022-0.1352-0.02360.1616-0.0293-0.03820.08250.01180.083444.7234.467723.5675
81.3069-0.84240.09052.52570.98111.3568-0.0577-0.3187-0.32990.26780.04830.40140.3425-0.27830.00930.0973-0.0660.01810.29630.08830.107439.554510.511441.0044
91.6597-1.050.14362.32740.38431.6883-0.0647-0.4163-0.31280.46690.12060.210.4066-0.1413-0.05590.1852-0.05580.00450.25240.11680.070844.90455.914744.7079
107.97380.73144.20673.53871.77994.16870.01620.2028-0.37850.22390.05710.32070.37850.1508-0.07330.1303-0.0418-0.0270.0490.03280.089746.2081-3.810433.7742
112.797-2.0970.79421.9351-0.38943.05840.0319-0.01070.1625-0.02420.0277-0.0047-0.2506-0.4786-0.05960.08530.0757-0.02880.2515-0.020.102432.352337.368228.8312
121.775-0.7303-0.11290.8942-0.08880.9415-0.0884-0.2330.2730.040.0518-0.1233-0.1614-0.0750.03660.05990.0291-0.03820.2148-0.05830.056146.027634.340138.3474
135.10290.9875-2.9211.3665-0.953510.37370.12930.05650.51320.15750.10590.0283-0.6412-0.089-0.23530.0790.0407-0.03110.034-0.03160.096540.635646.96430.5407
144.2348-1.0279-1.10291.32981.58062.56250.1080.3082-0.40530.1168-0.0753-0.08770.27360.2025-0.03270.11380.0734-0.02980.1982-0.02720.10318.454340.683748.0687
152.75850.0426-0.67980.86360.48511.36110.0963-0.2974-0.48970.3004-0.0636-0.11290.42050.157-0.03260.2562-0.0214-0.07480.14790.05660.111210.657639.167565.4768
163.0570.3763-0.45410.95210.19271.75610.0791-0.5336-0.33850.3906-0.044-0.1920.32090.3038-0.0350.23280.0264-0.10020.18970.0620.078717.190641.63169.2403
173.99342.34090.50979.81044.54593.3888-0.1346-0.1347-0.4189-0.20670.2303-0.27450.0860.3914-0.09570.09630.0685-0.04430.1026-0.01650.091126.70138.299658.6085
183.7371.19231.0161.00420.95892.97650.09890.0110.08080.04430.05270.09980.2321-0.3733-0.15170.0773-0.07690.00550.2211-0.02310.0916-16.312546.531253.3108
191.74560.87140.04931.137-0.17211.03980.1053-0.17670.23350.1451-0.14190.194-0.0247-0.17540.03660.0801-0.04350.03620.1782-0.06620.0491-6.795956.811862.8252
201.71131.84150.3164.2737-3.725510.516-0.0152-0.23050.2493-0.00180.10830.6083-0.2646-0.5681-0.09310.0165-0.002-0.03230.1711-0.01470.1797-20.412258.544154.9802
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 27
2X-RAY DIFFRACTION2A28 - 207
3X-RAY DIFFRACTION3A208 - 231
4X-RAY DIFFRACTION4B-1 - 27
5X-RAY DIFFRACTION5B28 - 215
6X-RAY DIFFRACTION6B216 - 230
7X-RAY DIFFRACTION7C-1 - 47
8X-RAY DIFFRACTION8C48 - 128
9X-RAY DIFFRACTION9C129 - 207
10X-RAY DIFFRACTION10C208 - 231
11X-RAY DIFFRACTION11D-1 - 27
12X-RAY DIFFRACTION12D28 - 215
13X-RAY DIFFRACTION13D216 - 230
14X-RAY DIFFRACTION14E-1 - 47
15X-RAY DIFFRACTION15E48 - 129
16X-RAY DIFFRACTION16E130 - 207
17X-RAY DIFFRACTION17E208 - 230
18X-RAY DIFFRACTION18F-1 - 27
19X-RAY DIFFRACTION19F28 - 215
20X-RAY DIFFRACTION20F216 - 230

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