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- PDB-4glf: Crystal structure of methylthioadenosine phosphorylase sourced fr... -

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Basic information

Entry
Database: PDB / ID: 4glf
TitleCrystal structure of methylthioadenosine phosphorylase sourced from an antarctic soil metagenomic library
ComponentsRsfP
KeywordsTRANSFERASE / methylthioadenosine phosphorylase / methylthioadenosine / rhodamine B / Metagenomic library Antarctic soil
Function / homology
Function and homology information


S-methyl-5'-thioadenosine phosphorylase / S-methyl-5-thioadenosine phosphorylase activity / L-methionine salvage from methylthioadenosine / purine ribonucleoside salvage / cytosol
Similarity search - Function
Methylthioadenosine phosphorylase (MTAP) / Purine phosphorylase, family 2, conserved site / Purine and other phosphorylases family 2 signature. / Nucleoside phosphorylase domain / Nucleoside phosphorylase domain / Phosphorylase superfamily / Nucleoside phosphorylase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-methyl-5'-thioadenosine phosphorylase
Similarity search - Component
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsBujacz, A. / Bujacz, G. / Cieslinski, H. / Bartasun, P.
CitationJournal: Plos One / Year: 2013
Title: A study on the interaction of rhodamine B with methylthioadenosine phosphorylase protein sourced from an antarctic soil metagenomic library.
Authors: Bartasun, P. / Cieslinski, H. / Bujacz, A. / Wierzbicka-Wos, A. / Kur, J.
History
DepositionAug 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RsfP


Theoretical massNumber of molelcules
Total (without water)32,1661
Polymers32,1661
Non-polymers00
Water3,441191
1
A: RsfP

A: RsfP

A: RsfP


Theoretical massNumber of molelcules
Total (without water)96,4973
Polymers96,4973
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area6230 Å2
ΔGint-21 kcal/mol
Surface area32340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.648, 80.648, 81.249
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-410-

HOH

21A-413-

HOH

31A-438-

HOH

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Components

#1: Protein RsfP


Mass: 32165.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Gene: rsfP / Plasmid: pBAD-Myc-HisA / Production host: Escherichia coli (E. coli) / Strain (production host): LMG194 / References: UniProt: C6KFA4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.37 Å3/Da / Density % sol: 48.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30%PPG400, 75mM MgCl2, BIS-TRIS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 26, 2010 / Details: mirrors
RadiationMonochromator: double crystal Si monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. all: 233379 / Num. obs: 20266 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.5 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 26.92
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 2.8 / Num. unique all: 1555 / % possible all: 74.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V4N

1v4n


Resolution: 1.98→50 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.956 / SU B: 7.256 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20884 1035 5.1 %RANDOM
Rwork0.15056 ---
all0.153 20266 --
obs0.15346 19185 96.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.636 Å2
Baniso -1Baniso -2Baniso -3
1-2.01 Å21 Å20 Å2
2--2.01 Å20 Å2
3----3.01 Å2
Refinement stepCycle: LAST / Resolution: 1.98→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2180 0 0 191 2371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022279
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.9593115
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7315304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.64325.05199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.02815387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5391512
X-RAY DIFFRACTIONr_chiral_restr0.1350.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211731
LS refinement shellResolution: 1.98→2.032 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 66 -
Rwork0.209 1050 -
obs--72.51 %
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)
12.6576-2.3211.37454.60871.71034.0861-0.2393-0.13490.4010.01160.0601-0.2686-0.4734-0.11640.17920.29180.03220.06620.1251-0.03640.269621.904751.954964.3191
22.5926-1.5821-0.54762.06470.73320.3999-0.0249-0.29460.35960.23780.0817-0.1235-0.11190.0074-0.05680.32990.01680.02460.0822-0.04570.119527.969244.367766.891
30.6948-0.4879-0.19991.5637-0.43012.3218-0.02510.02740.12090.0152-0.043-0.0187-0.245-0.05070.06810.04870.0172-0.0420.0316-0.01050.061628.133941.098454.3658
412.8302-8.87514.57918.4966-5.13583.2780.070.4026-0.05560.0783-0.1022-0.0155-0.080.00330.03210.02820.0267-0.01590.0452-0.01370.009430.676131.739247.975
51.93191.2168-0.60432.9672-0.53161.7823-0.0915-0.1852-0.07660.0247-0.04370.03550.1445-0.00030.13510.02760.00980.01960.0428-0.0210.05527.376424.585561.2605
62.7202-0.9853-0.15729.5305-3.65882.7167-0.12150.16920.1447-0.02870.27220.4812-0.237-0.4272-0.15070.07090.0597-0.03370.1063-0.01050.070920.680245.388445.4913
73.5504-1.65851.38292.4693-1.57811.5788-0.05650.0860.18420.00770.04160.0463-0.2873-0.12810.01490.14730.0513-0.00610.0575-0.0170.043435.536540.335747.3261
815.03-0.95475.3684.32132.85819.15760.02660.4359-0.307-0.395-0.09260.1988-0.0145-0.15070.0660.07950.02310.01440.06230.02180.055843.543431.352342.8156
95.33731.3568-3.46091.1008-1.72013.1795-0.04770.17780.13410.10670.0752-0.0099-0.1051-0.1491-0.02750.04950.0256-0.03290.0245-0.01520.05228.143833.924755.5295
105.23982.6622-1.44482.4778-1.88116.2711-0.3879-0.25450.0275-0.23780.0627-0.2841-0.07280.5480.32520.072-0.0118-0.00430.1426-0.03570.141932.318643.396748.9949
111.37913.93470.729712.08242.1940.4047-0.21150.20290.123-0.91740.2275-0.432-0.20780.0765-0.0160.8650.00440.06350.83030.08260.893347.621248.633645.3082
1210.40752.9113-1.2055.3064-0.18785.310.1471-0.31270.57250.1271-0.1036-0.0894-0.49180.3025-0.04350.20290.0602-0.00490.0764-0.00770.122424.307952.385951.4926
130.0401-0.1751-0.08524.4529-3.5014.2625-0.0170.0665-0.0618-0.09690.11770.52970.2522-0.5416-0.10070.0492-0.00460.04140.245-0.01970.214115.020224.918865.5312
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 36
2X-RAY DIFFRACTION2A37 - 76
3X-RAY DIFFRACTION3A77 - 113
4X-RAY DIFFRACTION4A114 - 120
5X-RAY DIFFRACTION5A121 - 140
6X-RAY DIFFRACTION6A141 - 160
7X-RAY DIFFRACTION7A161 - 179
8X-RAY DIFFRACTION8A180 - 193
9X-RAY DIFFRACTION9A194 - 212
10X-RAY DIFFRACTION10A213 - 223
11X-RAY DIFFRACTION11A224 - 239
12X-RAY DIFFRACTION12A240 - 265
13X-RAY DIFFRACTION13A266 - 297

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