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- PDB-3tde: Crystal structure of S-adenosylmethionine synthetase Rv1392 from ... -

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Basic information

Entry
Database: PDB / ID: 3tde
TitleCrystal structure of S-adenosylmethionine synthetase Rv1392 from Mycobacterium tuberculosis
ComponentsS-adenosylmethionine synthase
KeywordsTRANSFERASE / SSGCID / Seattle Structural Genomics Center for Infectious Disease / tuberculosis / AdoMet / SAM
Function / homology
Function and homology information


cell wall / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / zymogen binding / one-carbon metabolic process / peptidoglycan-based cell wall / magnesium ion binding / ATP binding / plasma membrane / cytosol
Similarity search - Function
GMP Synthetase; Chain A, domain 3 - #10 / S-adenosylmethionine synthetase / S-adenosylmethionine synthetase, N-terminal / S-adenosylmethionine synthetase, central domain / S-adenosylmethionine synthetase, C-terminal / S-adenosylmethionine synthetase, conserved site / S-adenosylmethionine synthetase superfamily / S-adenosylmethionine synthetase, N-terminal domain / S-adenosylmethionine synthetase, central domain / S-adenosylmethionine synthetase, C-terminal domain ...GMP Synthetase; Chain A, domain 3 - #10 / S-adenosylmethionine synthetase / S-adenosylmethionine synthetase, N-terminal / S-adenosylmethionine synthetase, central domain / S-adenosylmethionine synthetase, C-terminal / S-adenosylmethionine synthetase, conserved site / S-adenosylmethionine synthetase superfamily / S-adenosylmethionine synthetase, N-terminal domain / S-adenosylmethionine synthetase, central domain / S-adenosylmethionine synthetase, C-terminal domain / S-adenosylmethionine synthase signature 1. / S-adenosylmethionine synthase signature 2. / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
S-adenosylmethionine synthase / S-adenosylmethionine synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionAug 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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

Downloads & links

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Assembly

Deposited unit
A: S-adenosylmethionine synthase
B: S-adenosylmethionine synthase
C: S-adenosylmethionine synthase
D: S-adenosylmethionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,9995
Polymers173,9764
Non-polymers231
Water26,7341484
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11900 Å2
ΔGint-45 kcal/mol
Surface area49510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.880, 85.100, 245.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
S-adenosylmethionine synthase / AdoMet synthase / MAT / Methionine adenosyltransferase


Mass: 43493.973 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: metK, MT1437, MTCY21B4.09, Rv1392 / Production host: Escherichia coli (E. coli)
References: UniProt: P77899, UniProt: P9WGV1*PLUS, methionine adenosyltransferase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1484 / 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: 2.31 Å3/Da / Density % sol: 46.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: MytuD.01625.a.A1 PS00654 at 19.3 mL against JCSG + H8 focus screen 0.2 M NaCl, 0.1 M BisTris pH 5.2, 20% PEG 3350 with 20% ethylene glycol as cryo-protection reagent, crystal tracking ID ...Details: MytuD.01625.a.A1 PS00654 at 19.3 mL against JCSG + H8 focus screen 0.2 M NaCl, 0.1 M BisTris pH 5.2, 20% PEG 3350 with 20% ethylene glycol as cryo-protection reagent, crystal tracking ID 219374b3, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 30, 2011
Details: Si(111) Double Crystal Monochrometer. Adjustable focusing mirrors in K-B geometry
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 138002 / Num. obs: 137558 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 24.083 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 13.77
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.85-1.90.4443.62551709993199.7
1.9-1.950.3674.43549279825199.5
1.95-2.010.3065.27544769530199.7
2.01-2.070.266.29539949303199.5
2.07-2.140.2177.61527058974199.5
2.14-2.210.1858.87519888704199.7
2.21-2.290.16610.02505758438199.7
2.29-2.390.13811.72499218130199.8
2.39-2.490.12812.82486387801199.8
2.49-2.620.11314.44469397403199.7
2.62-2.760.116.26459507164199.8
2.76-2.930.08718.28439876737199.8
2.93-3.130.07720.85419496312199.7
3.13-3.380.06923.26399825933199.7
3.38-3.70.06126.39373765484199.8
3.7-4.140.05528.29346014955199.8
4.14-4.780.0529.98309884433199.7
4.78-5.850.04729.08265173760199.9
5.85-8.270.04228.85208432969199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å47.96 Å
Translation3 Å47.96 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RV2

3rv2


Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.1883 / WRfactor Rwork: 0.1603 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8946 / SU B: 4.518 / SU ML: 0.072 / SU R Cruickshank DPI: 0.1241 / SU Rfree: 0.1145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1939 6912 5 %RANDOM
Rwork0.1638 ---
obs0.1654 137558 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 52.32 Å2 / Biso mean: 19.0919 Å2 / Biso min: 8.12 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20 Å2
2---0.51 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11169 0 1 1484 12654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01911559
X-RAY DIFFRACTIONr_angle_refined_deg1.231.97315778
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.60451535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73623.485485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.238151882
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.32515101
X-RAY DIFFRACTIONr_chiral_restr0.0810.21869
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218769
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 455 -
Rwork0.199 9027 -
all-9482 -
obs--99.62 %
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)
10.1491-0.02110.03350.27980.04820.1998-0.0048-0.0057-0.0311-0.02940.00060.00050.00670.00140.00430.01330.00210.00260.0111-0.01010.030713.4526-13.3122.3198
20.1646-0.2447-0.02150.487-0.05850.13010.0290.0107-0.0218-0.1051-0.02750.03750.0016-0.0083-0.00150.0660.0112-0.01280.0144-0.00570.01637.9507-4.2639-11.1512
30.07550.0154-0.03490.3032-0.07060.1744-0.003-0.01420.0125-0.04510.00450.0029-0.00840.0046-0.00150.02410.00070.01460.01330.00780.026525.192914.16471.7504
40.2105-0.3940.03590.8145-0.06790.16470.0629-0.00410.0062-0.1658-0.0272-0.0551-0.03060.0301-0.03580.07330.0050.04790.02320.00790.040237.56570.0594-12.0162
50.1270.0687-0.11170.19090.07030.25940.0216-0.00030.00720.0216-0.01880.0211-0.04080.0128-0.00280.0251-0.01550.01360.0239-0.00940.02214.664113.59144.6448
60.27880.1812-0.13410.27860.06160.36920.00760.0234-0.00750.0654-0.01550.02690.0061-0.00760.00790.0486-0.01070.03160.0187-0.0030.0230.75571.047957.9709
70.0830.1245-0.08470.2284-0.17590.3657-0.0248-0.0181-0.0059-0.0139-0.0295-0.00470.04330.04690.05430.02790.01180.01590.0320.0190.019921.595-15.057844.4277
80.53150.4339-0.04660.38470.05180.51850.0317-0.0629-0.03770.041-0.0514-0.04050.01530.1350.01970.0124-0.0149-0.01220.07150.02720.014934.2549-2.931459.2438
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 225
2X-RAY DIFFRACTION2A226 - 403
3X-RAY DIFFRACTION3B5 - 275
4X-RAY DIFFRACTION4B276 - 403
5X-RAY DIFFRACTION5C5 - 275
6X-RAY DIFFRACTION6C276 - 403
7X-RAY DIFFRACTION7D5 - 276
8X-RAY DIFFRACTION8D277 - 403

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