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- PDB-9cbr: Methionine synthase from Thermus thermophilus HB8, Homocysteine, ... -

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Basic information

Entry
Database: PDB / ID: 9cbr
TitleMethionine synthase from Thermus thermophilus HB8, Homocysteine, Folate, and Cobalamin Domains, Catalytic Conformation (Hcy-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
COBALAMIN / 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID / : / ETHANAMINE / Methionine synthase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsYamada, K. / Menjdoza, 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, Homocysteine, Folate, and Cobalamin Domains, Catalytic Conformation (Hcy-on)
Authors: Menjdoza, J. / Yamada, K. / Koutmos, M.
History
DepositionJun 19, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release
Revision 2.0Sep 3, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_contact_author / pdbx_database_related / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_struct_assembly_gen.asym_id_list / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.dev_ideal_target / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_free / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _reflns.pdbx_number_measured_all / _software.version / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end / _struct_sheet.number_strands
Description: Model completeness
Details: Updated model to include previously unmodelled upper axial ligand present in the holoenzyme (non-native cofactor)
Provider: author / Type: Coordinate replacement

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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)97,7157
Polymers95,7111
Non-polymers2,0056
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.811, 115.101, 120.795
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 95710.578 Da / Num. of mol.: 1
Mutation: F110A, E123A, E124A, R268A, N283G, D651A, P652A, G653A, D759A, N774H, R826A
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

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Non-polymers , 6 types, 254 molecules

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


Mass: 459.456 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H25N7O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: K
#6: Chemical ChemComp-NEH / ETHANAMINE


Mass: 45.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H7N / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 20% PEG 3350, 0.1 M Tris (pH 8.5), and 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 10, 2022
Details: K-B pair of biomorph mirrors for vertical and horizontal focusing, with two horizontally deflecting mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.38→120.79 Å / Num. obs: 39748 / % possible obs: 98.8 % / Redundancy: 5.6 % / CC1/2: 0.908 / Rmerge(I) obs: 0.549 / Rpim(I) all: 0.251 / Rrim(I) all: 0.605 / Χ2: 1.05 / Net I/σ(I): 3.8
Reflection shellResolution: 2.38→2.47 Å / % possible obs: 89.4 % / Redundancy: 5.4 % / Rmerge(I) obs: 4.166 / Num. measured all: 19913 / Num. unique obs: 3707 / CC1/2: 0.221 / Rpim(I) all: 1.922 / Rrim(I) all: 4.604 / Χ2: 0.28 / Net I/σ(I) obs: 0.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
DIALSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→83.33 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.906 / SU B: 4.499 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21668 2021 5.1 %RANDOM
Rwork0.19456 ---
obs0.19565 37865 98.9 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.3 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2---0.26 Å20 Å2
3---0.72 Å2
Refinement stepCycle: 1 / Resolution: 2.38→83.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6646 0 130 248 7024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0126906
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166762
X-RAY DIFFRACTIONr_angle_refined_deg2.0561.8699377
X-RAY DIFFRACTIONr_angle_other_deg0.681.74815545
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5985872
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.759569
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.081101173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0970.21058
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028155
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021503
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_it2.2542.3033471
X-RAY DIFFRACTIONr_mcbond_other2.2542.3033471
X-RAY DIFFRACTIONr_mcangle_it3.374.1574334
X-RAY DIFFRACTIONr_mcangle_other3.374.1574335
X-RAY DIFFRACTIONr_scbond_it2.2842.4693435
X-RAY DIFFRACTIONr_scbond_other2.2842.4693436
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4034.4565044
X-RAY DIFFRACTIONr_long_range_B_refined7.23449.24112478
X-RAY DIFFRACTIONr_long_range_B_other7.23449.24112478
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.38→2.442 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 103 -
Rwork0.173 2403 -
obs--85.12 %
Refinement TLS params.Method: refined / Origin x: 8.163 Å / Origin y: -19.513 Å / Origin z: -18.645 Å
111213212223313233
T0.0391 Å2-0.0196 Å20.0049 Å2-0.179 Å20.0028 Å2--0.0517 Å2
L0.3165 °2-0.4611 °2-0.0766 °2-0.8801 °20.081 °2--0.1911 °2
S0.0241 Å °0.0576 Å °0.0967 Å °-0.0393 Å °0.0221 Å °-0.143 Å °0.01 Å °-0.0264 Å °-0.0462 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 872
2X-RAY DIFFRACTION1A901 - 905

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