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- PDB-2ydy: Crystal structure of human S-adenosylmethionine synthetase 2, bet... -

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Basic information

Entry
Database: PDB / ID: 2ydy
TitleCrystal structure of human S-adenosylmethionine synthetase 2, beta subunit in Orthorhombic crystal form
ComponentsMETHIONINE ADENOSYLTRANSFERASE 2 SUBUNIT BETA
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


methionine adenosyltransferase regulator activity / dTDP-4-dehydrorhamnose reductase activity / methionine adenosyltransferase complex / dTDP-rhamnose biosynthetic process / Methylation / S-adenosylmethionine biosynthetic process / extracellular polysaccharide biosynthetic process / one-carbon metabolic process / Ub-specific processing proteases / enzyme binding ...methionine adenosyltransferase regulator activity / dTDP-4-dehydrorhamnose reductase activity / methionine adenosyltransferase complex / dTDP-rhamnose biosynthetic process / Methylation / S-adenosylmethionine biosynthetic process / extracellular polysaccharide biosynthetic process / one-carbon metabolic process / Ub-specific processing proteases / enzyme binding / extracellular exosome / nucleus / cytosol
Similarity search - Function
dTDP-4-dehydrorhamnose reductase family / RmlD-like substrate binding domain / RmlD substrate 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
Methionine adenosyltransferase 2 subunit beta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.25 Å
AuthorsYue, W.W. / Shafqat, N. / Muniz, J.R.C. / Pike, A.C.W. / Chaikuad, A. / Allerston, C.K. / Gileadi, O. / von Delft, F. / Kavanagh, K.L. / Arrowsmith, C.H. ...Yue, W.W. / Shafqat, N. / Muniz, J.R.C. / Pike, A.C.W. / Chaikuad, A. / Allerston, C.K. / Gileadi, O. / von Delft, F. / Kavanagh, K.L. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Oppermann, U.
CitationJournal: Biochem.J. / Year: 2013
Title: Insight Into S-Adenosylmethionine Biosynthesis from the Crystal Structures of the Human Methionine Adenosyltransferase Catalytic and Regulatory Subunits.
Authors: Shafqat, N. / Muniz, J.R.C. / Pilka, E.S. / Papagrigoriou, E. / von Delft, F. / Oppermann, U. / Yue, W.W.
History
DepositionMar 25, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references / Refinement description / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: METHIONINE ADENOSYLTRANSFERASE 2 SUBUNIT BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1515
Polymers35,8281
Non-polymers3244
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.980, 111.770, 123.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1328-

CL

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Components

#1: Protein METHIONINE ADENOSYLTRANSFERASE 2 SUBUNIT BETA / DTDP-4-KETO-6-DEOXY-D-GLUCOSE 4-REDUCTASE / METHIONINE ADENOSYLTRANSFERASE II BETA / MAT II BETA S- ...DTDP-4-KETO-6-DEOXY-D-GLUCOSE 4-REDUCTASE / METHIONINE ADENOSYLTRANSFERASE II BETA / MAT II BETA S-ADENOSYLMETHIONINE SYNTHETASE 2\ / BETA SUBUNIT / MAT2B


Mass: 35827.738 Da / Num. of mol.: 1 / Fragment: RESIDUES 17-323
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q9NZL9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.5 Å3/Da / Density % sol: 50.81 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 9, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.17→61.61 Å / Num. obs: 15419 / % possible obs: 99.8 % / Observed criterion σ(I): 2.4 / Redundancy: 6.6 % / Biso Wilson estimate: 32.78 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 9.7
Reflection shellResolution: 2.17→2.29 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 2.4 / % possible all: 98.9

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
XDSdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.25→28.07 Å / Cor.coef. Fo:Fc: 0.9315 / Cor.coef. Fo:Fc free: 0.9141 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=SO4 CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=2099. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=15. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=SO4 CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=2099. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=15. NUMBER TREATED BY BAD NON-BONDED CONTACTS=1.
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 641 5.1 %RANDOM
Rwork0.1751 ---
obs0.1773 12589 99.8 %-
Displacement parametersBiso mean: 33.6 Å2
Baniso -1Baniso -2Baniso -3
1-7.5677 Å20 Å20 Å2
2--3.1742 Å20 Å2
3----10.7419 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.25→28.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2010 0 16 80 2106
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0092076HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.972823HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d946SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes51HARMONIC2
X-RAY DIFFRACTIONt_gen_planes304HARMONIC5
X-RAY DIFFRACTIONt_it2076HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.79
X-RAY DIFFRACTIONt_other_torsion2.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion272SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2416SEMIHARMONIC4
LS refinement shellResolution: 2.25→2.46 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2214 161 5.52 %
Rwork0.1846 2754 -
all0.1867 2915 -
obs--99.8 %
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)
10.00052.84682.14333.1999-0.6620.86720.00970.0222-0.1904-0.10580.14510.12320.2067-0.1814-0.1547-0.0608-0.0092-0.0362-0.1319-0.02570.0794-17.7109-19.83544.881
23.53640.43611.21984.66182.7281.06060.02650.1153-0.37590.002-0.02570.02790.2424-0.1655-0.0008-0.01230.0204-0.0375-0.1605-0.07650.0317-14.8985-26.92764.646
31.60352.88570.99912.1419-2.07643.71670.03460.0689-0.11610.0517-0.00120.01520.05550.0277-0.03330.29540.0537-0.0657-0.20050.0640.1498-9.6104-27.621116.744
42.6067-0.5842-0.26372.0805-0.05911.080.0352-0.3205-0.22480.3070.0489-0.10170.25570.2572-0.0841-0.05730.0055-0.0094-0.0490.0173-0.0107-5.5082-10.207321.0202
55.4287-2.34650.68261.4676-0.2281.36640.0901-0.2115-0.05270.13850.0293-0.04630.0466-0.061-0.1194-0.075-0.03360.0291-0.097-0.01920.062-21.0781-5.640514.9853
60.54070.47820.21630.67080.00830.8932-0.0111-0.0328-0.02310.04740.08010.0298-0.09370.1156-0.069-0.03670.0070.0074-0.0747-0.0115-0.0108-14.6068-0.681112.8514
70.0264-0.58560.45630.1014-0.06330.5257-0.0011-0.1139-0.03680.03140.00830.0078-0.01040.005-0.0072-0.005-0.0269-0.0148-0.0293-0.05790.0275-10.69961.273226.0404
80.0454-0.2720.42030.98730.29820.6245-0.02040.15350.1016-0.16710.0727-0.0994-0.17110.0412-0.0523-0.0387-0.00190.00430.0236-0.01030.0088-15.4651-1.63665.8918
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 28 - 48)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 49 - 92)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 93 - 128)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 129 - 170)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 171 - 211)
6X-RAY DIFFRACTION6(CHAIN A AND RESIDUE 288 - 292)
7X-RAY DIFFRACTION7(CHAIN A AND RESIDUE 288 - 292)
8X-RAY DIFFRACTION8(CHAIN A AND RESIDUE 293 - 324)

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