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- PDB-6bdy: Crystal Structure of the MetH Reactivation Domain bound to Sinefungin -

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Basic information

Entry
Database: PDB / ID: 6bdy
TitleCrystal Structure of the MetH Reactivation Domain bound to Sinefungin
ComponentsMethionine synthase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / C-terminal domain / reactivation domain / MetH-sinefungin / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


methionine synthase / methionine synthase activity / homocysteine metabolic process / methionine biosynthetic process / cobalamin binding / tetrahydrofolate metabolic process / tetrahydrofolate interconversion / methylation / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Cobalamin-dependent Methionine Synthase; domain 2 / Cobalamin-dependent Methionine Synthase, domain 2 / Cobalamin-dependent Methionine Synthase; domain 1 / Vitamin B12-dependent methionine synthase, activation domain / Vitamin B12-dependent methionine synthase, activation domain / Vitamin B12 dependent methionine synthase, activation domain / AdoMet activation domain profile. / Cobalamin-dependent methionine synthase / Methionine synthase, B12-binding domain / Vitamin B12-dependent methionine synthase, activation domain superfamily ...Cobalamin-dependent Methionine Synthase; domain 2 / Cobalamin-dependent Methionine Synthase, domain 2 / Cobalamin-dependent Methionine Synthase; domain 1 / Vitamin B12-dependent methionine synthase, activation domain / Vitamin B12-dependent methionine synthase, activation domain / Vitamin B12 dependent methionine synthase, activation domain / AdoMet activation domain profile. / Cobalamin-dependent methionine synthase / Methionine synthase, B12-binding domain / Vitamin B12-dependent methionine synthase, activation domain superfamily / B12-binding N-terminal domain profile. / B12 binding domain / Homocysteine-binding domain / Homocysteine-binding domain superfamily / Homocysteine S-methyltransferase / Homocysteine-binding domain profile. / Cobalamin (vitamin B12)-binding module, cap domain / B12 binding domain / Methionine synthase domain / B12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / Pterin-binding domain / Pterin binding enzyme / Pterin-binding domain profile. / Dihydropteroate synthase-like / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
SINEFUNGIN / Methionine synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.512 Å
AuthorsFick, R.J. / Vander Lee, L.P. / Trievel, R.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1508492 United States
CitationJournal: Biochemistry / Year: 2018
Title: Water-Mediated Carbon-Oxygen Hydrogen Bonding Facilitates S-Adenosylmethionine Recognition in the Reactivation Domain of Cobalamin-Dependent Methionine Synthase.
Authors: Fick, R.J. / Clay, M.C. / Vander Lee, L. / Scheiner, S. / Al-Hashimi, H. / Trievel, R.C.
History
DepositionOct 24, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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

Downloads & links

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Assembly

Deposited unit
A: Methionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2752
Polymers37,8931
Non-polymers3811
Water7,963442
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.350, 61.577, 139.877
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 Methionine synthase / / 5-methyltetrahydrofolate--homocysteine methyltransferase / Methionine synthase / vitamin-B12-dependent / MS


Mass: 37893.293 Da / Num. of mol.: 1 / Fragment: reactivation domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: metH, b4019, JW3979 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: P13009, methionine synthase
#2: Chemical ChemComp-SFG / SINEFUNGIN / ADENOSYL-ORNITHINE


Mass: 381.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N7O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.18 Å3/Da / Density % sol: 43.56 % / Mosaicity: 1.903 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 28% PEG 6000, 100mM Tris pH 7.3, 300mM magnesium acetate:15mg/mL protein, 3mM sinefungin, 10mM Tris 7.2, 10mM EDTA, 2:2uL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 51658 / % possible obs: 98.5 % / Redundancy: 5.9 % / Biso Wilson estimate: 15.52 Å2 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.027 / Rrim(I) all: 0.067 / Χ2: 1.021 / Net I/σ(I): 13.7 / Num. measured all: 302238
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.534.50.2822690.9590.140.3150.93287.7
1.53-1.554.80.25224190.9660.1230.2820.99294.3
1.55-1.585.30.23625120.9780.1080.261.0296.9
1.58-1.625.80.21825490.9780.0980.241.01599.8
1.62-1.6560.19826130.9870.0870.2171.024100
1.65-1.696.20.17225420.990.0750.1881.052100
1.69-1.736.20.15726260.990.0690.1721.063100
1.73-1.786.20.13525700.9910.0590.1471.022100
1.78-1.836.30.12525930.9920.0540.1371.082100
1.83-1.896.20.11125980.9930.0490.1220.99399.9
1.89-1.966.20.09925980.9950.0440.1090.994100
1.96-2.046.10.09126000.9950.040.11.02100
2.04-2.136.10.08226010.9960.0360.091.03399.9
2.13-2.2460.07526480.9960.0330.0821.07799.9
2.24-2.3860.0726200.9950.0310.0771.038100
2.38-2.565.90.06726310.9950.030.0730.98599.8
2.56-2.825.80.05926220.9960.0270.0651.03599.8
2.82-3.235.70.05326730.9970.0240.0581.04699.8
3.23-4.075.80.04526870.9980.020.0490.97399.3
4.07-505.50.03726870.9980.0170.0410.96193.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.36 Å32.55 Å
Translation5.36 Å32.55 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASER2.6.0phasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 1MSK

1msk


Resolution: 1.512→32.553 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 19.51
RfactorNum. reflection% reflection
Rfree0.1859 2579 5 %
Rwork0.1437 --
obs0.1458 51571 97.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.03 Å2 / Biso mean: 24.2995 Å2 / Biso min: 10.04 Å2
Refinement stepCycle: final / Resolution: 1.512→32.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2563 0 27 442 3032
Biso mean--18.79 38.75 -
Num. residues----326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012712
X-RAY DIFFRACTIONf_angle_d1.0423711
X-RAY DIFFRACTIONf_chiral_restr0.063394
X-RAY DIFFRACTIONf_plane_restr0.008489
X-RAY DIFFRACTIONf_dihedral_angle_d3.3212170
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5123-1.54130.3131080.23112056216475
1.5413-1.57280.20961350.1742557269294
1.5728-1.6070.20281420.15122697283998
1.607-1.64440.19941440.134327252869100
1.6444-1.68550.19051430.129327452888100
1.6855-1.73110.191450.127627532898100
1.7311-1.7820.21921440.129727402884100
1.782-1.83950.191460.137227652911100
1.8395-1.90530.20521450.140627562901100
1.9053-1.98150.19071450.13927552900100
1.9815-2.07170.18851470.138827762923100
2.0717-2.18090.18751440.138927602904100
2.1809-2.31750.18931470.139427822929100
2.3175-2.49640.19651480.148128042952100
2.4964-2.74750.17661480.155128142962100
2.7475-3.14480.20051480.154828142962100
3.1448-3.9610.17891500.13122842299299
3.961-32.56040.15371500.14652851300195

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