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- PDB-1umy: BHMT from rat liver -

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Basic information

Entry
Database: PDB / ID: 1umy
TitleBHMT from rat liver
ComponentsBetaine--homocysteine S-methyltransferase 1
KeywordsTRANSFERASE / METHIONINE SYNTHESIS / HOMOCYSTEINE METABOLISM / BETAINE / METHYLTRANSFERASE / ZINC
Function / homology
Function and homology information


Choline catabolism / betaine-homocysteine S-methyltransferase / amino-acid betaine metabolic process / betaine-homocysteine S-methyltransferase activity / L-methionine salvage / Sulfur amino acid metabolism / amino-acid betaine catabolic process / protein methylation / methionine biosynthetic process / response to organonitrogen compound ...Choline catabolism / betaine-homocysteine S-methyltransferase / amino-acid betaine metabolic process / betaine-homocysteine S-methyltransferase activity / L-methionine salvage / Sulfur amino acid metabolism / amino-acid betaine catabolic process / protein methylation / methionine biosynthetic process / response to organonitrogen compound / methyltransferase activity / protein-containing complex binding / protein-containing complex / extracellular exosome / zinc ion binding / cytosol
Similarity search - Function
Betaine-homocysteine S-methyltransferase, BHMT / Homocysteine-binding-like domain / Homocysteine-binding domain / Homocysteine-binding domain superfamily / Homocysteine S-methyltransferase / Homocysteine-binding domain profile. / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Betaine--homocysteine S-methyltransferase 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGonzalez, B. / Pajares, M.A. / Sanz-Aparicio, J.
Citation
Journal: J. Mol. Biol. / Year: 2004
Title: Crystal structure of rat liver betaine homocysteine s-methyltransferase reveals new oligomerization features and conformational changes upon substrate binding.
Authors: Gonzalez, B. / Pajares, M.A. / Martinez-Ripoll, M. / Blundell, T.L. / Sanz-Aparicio, J.
#1: Journal: Biochem.J. / Year: 2003
Title: Active-Site Mutagenesis Study of Rat Liver Betaine Homocysteine S-Methyltransferase
Authors: Gonzalez, B. / Garrido, F. / Gasset, M. / Sanz-Aparicio, J. / Pajares, M.A.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Crystallization and Preliminary X-Ray Study of Recombinant Betaine-Homocysteine S-Methyltransferase from Rat Liver
Authors: Gonzalez, B. / Pajares, M.A. / Too, P. / Garrido, F. / Blundell, T.L. / Sanz-Aparicio, J.
History
DepositionSep 2, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 6, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 5, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_src_gen / pdbx_entity_src_syn / struct_ref
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity.pdbx_description / _entity.src_method / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Betaine--homocysteine S-methyltransferase 1
B: Betaine--homocysteine S-methyltransferase 1
C: Betaine--homocysteine S-methyltransferase 1
D: Betaine--homocysteine S-methyltransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,64010
Polymers180,2224
Non-polymers4186
Water9,692538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)57.830, 149.270, 96.250
Angle α, β, γ (deg.)90.00, 92.92, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99965, 0.00909, -0.02474), (0.00148, -0.91771, -0.39725), (-0.02631, -0.39715, 0.91738)29.46989, -27.36963, -5.39027
2given(-0.96255, -0.26019, -0.07618), (-0.26924, 0.88439, 0.38126), (-0.03183, 0.38749, -0.92133)25.17547, 9.33094, -28.57009
3given(0.96104, 0.25356, 0.11005), (0.25362, -0.96721, 0.01369), (0.10991, 0.01475, -0.99383)5.30163, -24.58447, -35.67911

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Components

#1: Protein
Betaine--homocysteine S-methyltransferase 1


Mass: 45055.410 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: ZN BOUND FORM / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Bhmt / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O09171, betaine-homocysteine S-methyltransferase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 538 / Source method: isolated from a natural source / Formula: H2O
Compound detailsINVOLVED IN THE REGULATION OF HOMOCYSTEINE METABOLISM. CONVERTS HOMOCYSTEINE AND BETAINE TO ...INVOLVED IN THE REGULATION OF HOMOCYSTEINE METABOLISM. CONVERTS HOMOCYSTEINE AND BETAINE TO DIMETHYLGLYCINE AND METHIONINE.

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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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growpH: 8.5 / Details: 16% PEG 1500, PH=8.5, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.004
DetectorDetector: CCD / Date: Apr 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.004 Å / Relative weight: 1
ReflectionResolution: 2.5→49 Å / Num. obs: 58532 / % possible obs: 99.7 % / Observed criterion σ(I): 4 / Redundancy: 4 % / Biso Wilson estimate: 45.8 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 6.5
Reflection shellResolution: 2.5→2.58 Å / Redundancy: 4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 1.5 / % possible all: 99.1

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LT8

1lt8


Resolution: 2.5→48.4 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.291 5548 10 %RANDOM
Rwork0.253 ---
obs0.253 54654 97.1 %-
Solvent computationSolvent model: FLAT / Bsol: 61.82 Å2 / ksol: 0.356894 e/Å3
Displacement parametersBiso mean: 50.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.45 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 2.5→48.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11803 0 12 538 12353
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.393 949 10 %
Rwork0.333 8300 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN_REP.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP

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