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- PDB-9cbo: Methionine synthase from Thermus thermophilus HB8, Folate and Cob... -

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Basic information

Entry
Database: PDB / ID: 9cbo
TitleMethionine synthase from Thermus thermophilus HB8, Folate and Cobalamin Domains, Pre-Catalytic Conformation (Pre-Fol-on)
ComponentsMethionine synthase
KeywordsTRANSFERASE / Methyl transferase / cobalamin-dependent / cobalamin binding / one-carbon metabolism
Function / homology
Function and homology information


methionine synthase / methionine synthase activity / homocysteine metabolic process / cobalamin binding / tetrahydrofolate metabolic process / methylation / zinc ion binding / cytosol
Similarity search - Function
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 ...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
Similarity search - Domain/homology
CO-METHYLCOBALAMIN / Methionine synthase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.34 Å
AuthorsYamada, K. / Mendoza, J. / Koutmos, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1945174 United States
CitationJournal: To Be Published
Title: Methionine synthase from Thermus thermophilus HB8, Folate and Cobalamin Domains, Pre-Catalytic Conformation (Pre-Fol-on)
Authors: Mendoza, J. / Yamada, K. / Koutmos, M.
History
DepositionJun 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methionine synthase
B: Methionine synthase
C: Methionine synthase
D: Methionine synthase
E: Methionine synthase
F: Methionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)348,78118
Polymers340,1626
Non-polymers8,61912
Water1,946108
1
A: Methionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1303
Polymers56,6941
Non-polymers1,4362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Methionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1303
Polymers56,6941
Non-polymers1,4362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Methionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2224
Polymers56,6941
Non-polymers1,5293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Methionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0382
Polymers56,6941
Non-polymers1,3441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Methionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1303
Polymers56,6941
Non-polymers1,4362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Methionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1303
Polymers56,6941
Non-polymers1,4362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)187.769, 187.769, 325.547
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Methionine synthase / 5-methyltetrahydrofolate--homocysteine methyltransferase


Mass: 56693.609 Da / Num. of mol.: 6 / Mutation: D759A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: ATCC 27634 / DSM 579 / HB8 / Gene: TTHA0618 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SKM5, methionine synthase
#2: Chemical
ChemComp-COB / CO-METHYLCOBALAMIN


Mass: 1344.382 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C63H91CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 4.21 Å3/Da / Density % sol: 70.82 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG 3350, 0.1 M Tris (pH 8.5), and 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MAR CCD 300 mm / Detector: CCD / Date: Dec 13, 2015
Details: K-B pair of biomorph mirrors for vertical and horizontal focusing
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.34→325.55 Å / Num. obs: 85017 / % possible obs: 99.9 % / Redundancy: 8.3 % / CC1/2: 0.986 / Rmerge(I) obs: 0.24 / Rpim(I) all: 0.087 / Rrim(I) all: 0.256 / Χ2: 0.98 / Net I/σ(I): 6.7 / Num. measured all: 702906
Reflection shellResolution: 3.34→3.4 Å / % possible obs: 98.1 % / Redundancy: 8.4 % / Rmerge(I) obs: 2.194 / Num. measured all: 36503 / Num. unique obs: 4350 / CC1/2: 0.428 / Rpim(I) all: 0.787 / Rrim(I) all: 2.333 / Χ2: 1.04 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
DIALSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.34→163.18 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.942 / SU B: 51.264 / SU ML: 0.36 / Cross valid method: THROUGHOUT / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.216 4226 5 %RANDOM
Rwork0.17316 ---
obs0.17532 80679 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 118.474 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å2-0 Å2
2--0.48 Å20 Å2
3----0.95 Å2
Refinement stepCycle: 1 / Resolution: 3.34→163.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23842 0 588 110 24540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01224876
X-RAY DIFFRACTIONr_bond_other_d0.0010.01624776
X-RAY DIFFRACTIONr_angle_refined_deg2.6331.9133762
X-RAY DIFFRACTIONr_angle_other_deg0.6991.78456928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61953050
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.5015222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.766104456
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0920.23824
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0229064
X-RAY DIFFRACTIONr_gen_planes_other0.0020.025452
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_it11.8387.18912218
X-RAY DIFFRACTIONr_mcbond_other11.8387.18912218
X-RAY DIFFRACTIONr_mcangle_it16.60612.94215262
X-RAY DIFFRACTIONr_mcangle_other16.60612.94215263
X-RAY DIFFRACTIONr_scbond_it13.4267.8912658
X-RAY DIFFRACTIONr_scbond_other13.4267.89112659
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other18.74114.17918501
X-RAY DIFFRACTIONr_long_range_B_refined21.60988.99103404
X-RAY DIFFRACTIONr_long_range_B_other21.61188.99103390
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.34→3.425 Å
RfactorNum. reflection% reflection
Rfree0.335 278 -
Rwork0.322 5840 -
obs--98.66 %
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)
11.10830.90390.06970.81-0.06220.2730.1432-0.16080.07620.1012-0.16030.041-0.12170.02740.01710.34880.05640.07140.70920.12320.040919.77-33.607-57.933
21.06210.9929-0.06431.1276-0.44720.825-0.0274-0.0320.1044-0.14310.03570.10470.0382-0.1361-0.00840.6990.1176-0.12080.1861-0.010.2057-46.706-23.651-99.695
31.50080.52340.34590.878-0.44760.7427-0.0023-0.263-0.0843-0.05640.07330.0004-0.0888-0.1583-0.0710.36010.04310.09140.5280.08780.0501-26.078-43.128-57.226
43.9858-1.1596-0.25640.55430.0480.1316-0.1911-0.7207-0.08990.12750.1351-0.01060.08990.0850.05590.3906-0.08520.00150.69040.22750.0933-19.737-57.684-31.128
52.27560.1131-0.74190.11750.03442.40040.05830.11440.1228-0.1285-0.2996-0.0176-0.1792-0.74940.24130.16740.32550.05641.1198-0.21270.2389-22.8341.922-58.666
60.4137-0.9764-0.0683.4872-0.21890.35270.0630.1437-0.073-0.2333-0.21180.16570.0720.040.14881.0058-0.0352-0.16320.11670.04920.1263-44.00217.72-134.861
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A364 - 901
2X-RAY DIFFRACTION2B364 - 901
3X-RAY DIFFRACTION3C364 - 901
4X-RAY DIFFRACTION4D367 - 901
5X-RAY DIFFRACTION5E367 - 901
6X-RAY DIFFRACTION6F364 - 901

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