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- PDB-3iml: Crystal Structure Of S-Adenosylmethionine Synthetase From Burkhol... -

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Basic information

Entry
Database: PDB / ID: 3iml
TitleCrystal Structure Of S-Adenosylmethionine Synthetase From Burkholderia Pseudomallei
ComponentsS-adenosylmethionine synthetase
KeywordsTRANSFERASE / S-adenosylmethionine synthetase / structural genomics / ATP-binding / Cobalt / Magnesium / Metal-binding / Nucleotide-binding / One-carbon metabolism / Potassium / Seattle Structural Genomics Center for Infectious Disease / SSGCID
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 speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsStaker, B.L. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionAug 10, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Sep 6, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-adenosylmethionine synthetase
B: S-adenosylmethionine synthetase
C: S-adenosylmethionine synthetase
D: S-adenosylmethionine synthetase


Theoretical massNumber of molelcules
Total (without water)171,9544
Polymers171,9544
Non-polymers00
Water2,396133
1
A: S-adenosylmethionine synthetase
B: S-adenosylmethionine synthetase


Theoretical massNumber of molelcules
Total (without water)85,9772
Polymers85,9772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-24 kcal/mol
Surface area25100 Å2
MethodPISA
2
C: S-adenosylmethionine synthetase
D: S-adenosylmethionine synthetase


Theoretical massNumber of molelcules
Total (without water)85,9772
Polymers85,9772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-20 kcal/mol
Surface area23610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)236.303, 119.443, 65.353
Angle α, β, γ (deg.)90.00, 105.98, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 42988.406 Da / Num. of mol.: 4 / Fragment: S-adenosylmethionine synthetase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: metK, BPSL0212 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q63YH5, methionine adenosyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: HAMPTON CRYSTAL SCREEN HT CONDITION B11. 100 MM HEPES PH 7.5, 30% PEG-400, 200 MM MGCL2. PROTEIN CONCENTRATION 26 MG/ML, VAPOR DIFFUSIONI, SITTING DROP, TEMPERATURE 293K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 29, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 71326 / % possible obs: 98.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 9.6
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.395 / % possible all: 82.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Swissmodel based on PDB entry 1RG9

1rg9


Resolution: 2.35→28.31 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.914 / SU B: 17.619 / SU ML: 0.186 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.337 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.256 3602 5.1 %RANDOM
Rwork0.218 ---
obs0.22 71117 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.53 Å2
Baniso -1Baniso -2Baniso -3
1--2.79 Å20 Å2-1.99 Å2
2---2.01 Å20 Å2
3---3.7 Å2
Refinement stepCycle: LAST / Resolution: 2.35→28.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10366 0 0 133 10499
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02210570
X-RAY DIFFRACTIONr_bond_other_d0.0010.027068
X-RAY DIFFRACTIONr_angle_refined_deg1.241.97414368
X-RAY DIFFRACTIONr_angle_other_deg0.881317246
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.28951367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.89923.51433
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.534151682
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8841578
X-RAY DIFFRACTIONr_chiral_restr0.0730.21659
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111868
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022082
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5321.56838
X-RAY DIFFRACTIONr_mcbond_other0.0921.52801
X-RAY DIFFRACTIONr_mcangle_it1210948
X-RAY DIFFRACTIONr_scbond_it1.39733732
X-RAY DIFFRACTIONr_scangle_it2.2814.53419
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 217 -
Rwork0.288 4033 -
obs--79.25 %
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)
11.9751-0.57270.75291.246-0.74711.6273-0.00770.22140.02510.0219-0.0304-0.0348-0.02880.14110.03810.14890.03630.00650.1313-0.04720.0313-34.819141.024317.1592
21.9374-0.34410.43941.6927-0.22761.4631-0.0972-0.2660.31160.0990.1561-0.1154-0.05610.072-0.05890.16180.04610.02930.236-0.14960.1348-39.526659.629532.5719
31.4963-1.37210.31513.7209-0.85461.1820.15350.1415-0.3739-0.35410.08510.60090.2031-0.0426-0.23860.1644-0.0417-0.09970.12560.06150.2858-84.368352.2086-4.6105
41.61271.1260.13313.12210.00551.57-0.0331-0.05390.20610.03520.14210.4376-0.0362-0.2171-0.10890.1109-0.0016-0.00340.13260.11060.2908-91.570647.161319.4556
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 386
2X-RAY DIFFRACTION2B5 - 387
3X-RAY DIFFRACTION3C5 - 378
4X-RAY DIFFRACTION4D5 - 378

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