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- PDB-5voo: Methionine synthase folate-binding domain with methyltetrahydrofo... -

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Basic information

Entry
Database: PDB / ID: 5voo
TitleMethionine synthase folate-binding domain with methyltetrahydrofolate from Thermus thermophilus HB8
Components5-methyltetrahydrofolate homocysteine S-methyltransferase
KeywordsTRANSFERASE / METHYLTRANSFERASE / pterin binding / B12 binding / OXIDOREDUCTASE
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
5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID / DI(HYDROXYETHYL)ETHER / Methionine synthase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKoutmos, M. / Yamada, K.
Funding support United States, 1items
OrganizationGrant numberCountry
American Heart Association13SDG14560056 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: The folate-binding module of Thermus thermophilus cobalamin-dependent methionine synthase displays a distinct variation of the classical TIM barrel: a TIM barrel with a `twist'.
Authors: Yamada, K. / Koutmos, M.
History
DepositionMay 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 4, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5-methyltetrahydrofolate homocysteine S-methyltransferase
B: 5-methyltetrahydrofolate homocysteine S-methyltransferase
C: 5-methyltetrahydrofolate homocysteine S-methyltransferase
D: 5-methyltetrahydrofolate homocysteine S-methyltransferase
E: 5-methyltetrahydrofolate homocysteine S-methyltransferase
F: 5-methyltetrahydrofolate homocysteine S-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,45824
Polymers198,0966
Non-polymers3,36218
Water5,801322
1
A: 5-methyltetrahydrofolate homocysteine S-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5806
Polymers33,0161
Non-polymers5645
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 5-methyltetrahydrofolate homocysteine S-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6835
Polymers33,0161
Non-polymers6674
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 5-methyltetrahydrofolate homocysteine S-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5113
Polymers33,0161
Non-polymers4952
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 5-methyltetrahydrofolate homocysteine S-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6054
Polymers33,0161
Non-polymers5893
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: 5-methyltetrahydrofolate homocysteine S-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5823
Polymers33,0161
Non-polymers5662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: 5-methyltetrahydrofolate homocysteine S-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4983
Polymers33,0161
Non-polymers4822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)188.463, 188.463, 247.137
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
5-methyltetrahydrofolate homocysteine S-methyltransferase


Mass: 33016.051 Da / Num. of mol.: 6 / Fragment: folate-binding domain residues 353-648
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHA0618 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SKM5

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Non-polymers , 6 types, 340 molecules

#2: Chemical
ChemComp-C2F / 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID


Mass: 459.456 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H25N7O6
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 3.2 Å3/Da / Density % sol: 61.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M sodium citrate pH 4.5, 22 % polyethylene glycol 3350, 0.2 M tri-sodium citrate, soaked with 6S-methyltetrahydrofolate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 18, 2016
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.4→163.21 Å / Num. obs: 100615 / % possible obs: 99.4 % / Redundancy: 4.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.048 / Net I/σ(I): 8.93
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 1.92 / Num. unique obs: 4857 / CC1/2: 0.651 / Rpim(I) all: 0.342 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VON

5von


Resolution: 2.4→163.21 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.356 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.273 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22972 5056 5 %RANDOM
Rwork0.19039 ---
obs0.19235 95477 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.272 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20.18 Å20 Å2
2--0.35 Å20 Å2
3----1.15 Å2
Refinement stepCycle: 1 / Resolution: 2.4→163.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13257 0 232 322 13811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01913731
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213606
X-RAY DIFFRACTIONr_angle_refined_deg1.3632.01518561
X-RAY DIFFRACTIONr_angle_other_deg0.917330990
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04351685
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.38422.695616
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.683152426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.28415152
X-RAY DIFFRACTIONr_chiral_restr0.070.22111
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02115235
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022961
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_it2.3294.7976764
X-RAY DIFFRACTIONr_mcbond_other2.3274.7966760
X-RAY DIFFRACTIONr_mcangle_it3.7267.198435
X-RAY DIFFRACTIONr_mcangle_other3.7267.198434
X-RAY DIFFRACTIONr_scbond_it2.6875.1946967
X-RAY DIFFRACTIONr_scbond_other2.6875.1966933
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5267.63710077
X-RAY DIFFRACTIONr_long_range_B_refined6.26255.26414458
X-RAY DIFFRACTIONr_long_range_B_other6.26455.26414377
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.398→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 356 -
Rwork0.277 6925 -
obs--98.99 %

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