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- PDB-3rv2: Crystal structure of S-adenosylmethionine synthetase from Mycobac... -

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Basic information

Entry
Database: PDB / ID: 3rv2
TitleCrystal structure of S-adenosylmethionine synthetase from Mycobacterium marinum
ComponentsS-adenosylmethionine synthase
KeywordsTRANSFERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / SAM / S-adenosylmethionine / AdoMet / AdoMet synthase / methyl donor / methylation
Function / homology
Function and homology information


methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / one-carbon metabolic process / magnesium ion binding / ATP binding / cytoplasm
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
Similarity search - Component
Biological speciesMycobacterium marinum M (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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
DepositionMay 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Sep 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,41911
Polymers86,8662
Non-polymers5539
Water9,134507
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-22 kcal/mol
Surface area26200 Å2
MethodPISA
2
A: S-adenosylmethionine synthase
B: S-adenosylmethionine synthase
hetero molecules

A: S-adenosylmethionine synthase
B: S-adenosylmethionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,83722
Polymers173,7324
Non-polymers1,10518
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area15100 Å2
ΔGint-55 kcal/mol
Surface area48680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.600, 196.230, 59.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 43432.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum M (bacteria) / Strain: M / Gene: metK, MMAR_2205 / Production host: Escherichia coli (E. coli) / References: UniProt: B2HP50, methionine adenosyltransferase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 507 / 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: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MymaA.01625.a.A1 PW30103 at 40.19 mg/mL against JCSG+ screen condition E11, 0.16 M calcium acetate, 80 mM sodium cacodylate pH 6.5, 14.4% PEG 8000, 20% glycerol and 25% ethylene glycol as ...Details: MymaA.01625.a.A1 PW30103 at 40.19 mg/mL against JCSG+ screen condition E11, 0.16 M calcium acetate, 80 mM sodium cacodylate pH 6.5, 14.4% PEG 8000, 20% glycerol and 25% ethylene glycol as additional cryo-protectant, crystal tracking ID 220762e11, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 62515 / Num. obs: 61471 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 26.298 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 29.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2-2.054.60.1687.62176694572387184.7
2.05-2.110.159.6420682414293.6
2.11-2.170.13312.2248484302100
2.17-2.240.1214.0225365421499.9
2.24-2.310.10815.9123667407099.6
2.31-2.390.08918.24238103943100
2.39-2.480.0820.2723151382199.9
2.48-2.580.07322.2422337369699.9
2.58-2.70.06425.21211473518100
2.7-2.830.05229.5520297336499.9
2.83-2.980.04633.0119633326099.9
2.98-3.160.03938.3918234304299.9
3.16-3.380.03443.96172632895100
3.38-3.650.02951.7415500267699.9
3.65-40.02657.2513887247999.8
4-4.470.02263.9313225227299.8
4.47-5.160.02364.5811532201899.9
5.16-6.320.02260.029657171199.9
6.32-8.940.01767.167896137899.9
8.940.01371.8424879998.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 50.99 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å49.06 Å
Translation3 Å49.06 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3IML

3iml


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.1741 / WRfactor Rwork: 0.1464 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9027 / SU B: 6.052 / SU ML: 0.078 / SU R Cruickshank DPI: 0.1367 / SU Rfree: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.187 3101 5.1 %RANDOM
Rwork0.155 ---
obs0.1566 61296 98.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 52.82 Å2 / Biso mean: 21.4777 Å2 / Biso min: 5.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.99 Å20 Å20 Å2
2---1.27 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5626 0 31 507 6164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225781
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.9757866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9735754
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39823.443244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81215929
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6861551
X-RAY DIFFRACTIONr_chiral_restr0.0950.2923
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214375
X-RAY DIFFRACTIONr_mcbond_it0.6781.53714
X-RAY DIFFRACTIONr_mcangle_it1.23925993
X-RAY DIFFRACTIONr_scbond_it2.3632067
X-RAY DIFFRACTIONr_scangle_it3.8584.51867
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 196 -
Rwork0.177 3654 -
all-3850 -
obs--84.41 %
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)
10.17720.0066-0.05980.83270.05260.73530.01310.0034-0.002-0.1379-0.0184-0.0857-0.03560.02240.00540.0412-0.00440.00220.01980.01180.033941.110212.91016.9958
20.67260.15750.06231.09780.14360.7072-0.0133-0.01380.02540.01020.0184-0.1926-0.20860.0867-0.00510.0931-0.03960.00280.0183-0.00730.044547.194733.432215.4614
30.27660.07520.37721.34430.48781.3987-0.0079-0.02370.0037-0.1447-0.10350.0859-0.2386-0.2080.11140.12680.0508-0.01020.0541-0.01120.02527.811333.8513-0.1316
40.5981-0.33670.03840.52790.11530.7185-0.0708-0.0317-0.06590.10570.0610.0537-0.0183-0.02110.00980.03450.02150.01370.03810.00050.028828.69398.2726.2097
50.64090.35680.25141.02460.25030.7552-0.03830.00360.0125-0.0170.01340.1793-0.1119-0.18980.02480.02750.04970.00120.09920.00590.046311.006220.277517.7687
60.756-0.4326-0.07181.12570.09720.8133-0.02120.03150.02920.14950.0006-0.0558-0.1455-0.00960.02050.09650.0394-0.00020.03110.00970.006825.884633.322233.4918
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 106
2X-RAY DIFFRACTION2A133 - 276
3X-RAY DIFFRACTION3A277 - 403
4X-RAY DIFFRACTION4B5 - 106
5X-RAY DIFFRACTION5B133 - 276
6X-RAY DIFFRACTION6B277 - 403

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