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- PDB-1lt8: Reduced Homo sapiens Betaine-Homocysteine S-Methyltransferase in ... -

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Basic information

Entry
Database: PDB / ID: 1lt8
TitleReduced Homo sapiens Betaine-Homocysteine S-Methyltransferase in Complex with S-(delta-carboxybutyl)-L-Homocysteine
ComponentsBETAINE-HOMOCYSTEINE METHYLTRANSFERASE
KeywordsTRANSFERASE / homocysteine metabolism / homocysteinemia / zinc / thiol alkyl transfer
Function / homology
Function and homology information


regulation of homocysteine metabolic process / betaine-homocysteine S-methyltransferase / amino-acid betaine metabolic process / betaine-homocysteine S-methyltransferase activity / L-methionine salvage / amino-acid betaine catabolic process / Sulfur amino acid metabolism / Choline catabolism / 'de novo' L-methionine biosynthetic process / protein methylation ...regulation of homocysteine metabolic process / betaine-homocysteine S-methyltransferase / amino-acid betaine metabolic process / betaine-homocysteine S-methyltransferase activity / L-methionine salvage / amino-acid betaine catabolic process / Sulfur amino acid metabolism / Choline catabolism / 'de novo' L-methionine biosynthetic process / protein methylation / extracellular exosome / zinc ion binding / nucleus / 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
S-(D-CARBOXYBUTYL)-L-HOMOCYSTEINE / CITRIC ACID / Betaine--homocysteine S-methyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsEvans, J.C. / Huddler, D.P. / Jiracek, J. / Castro, C. / Millian, N.S. / Garrow, T.A. / Ludwig, M.L.
CitationJournal: Structure / Year: 2002
Title: Betaine-homocysteine methyltransferase: zinc in a distorted barrel.
Authors: Evans, J.C. / Huddler, D.P. / Jiracek, J. / Castro, C. / Millian, N.S. / Garrow, T.A. / Ludwig, M.L.
History
DepositionMay 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETAINE-HOMOCYSTEINE METHYLTRANSFERASE
B: BETAINE-HOMOCYSTEINE METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6748
Polymers89,6882
Non-polymers9866
Water7,764431
1
A: BETAINE-HOMOCYSTEINE METHYLTRANSFERASE
B: BETAINE-HOMOCYSTEINE METHYLTRANSFERASE
hetero molecules

A: BETAINE-HOMOCYSTEINE METHYLTRANSFERASE
B: BETAINE-HOMOCYSTEINE METHYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,34716
Polymers179,3764
Non-polymers1,97112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)109.702, 90.836, 88.403
Angle α, β, γ (deg.)90.00, 122.28, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein BETAINE-HOMOCYSTEINE METHYLTRANSFERASE / BETAINE-HOMOCYSTEINE S-METHYLTRANSFERASE


Mass: 44844.020 Da / Num. of mol.: 2 / Mutation: P2A, C104A, C131A, C186A, C201A, C256A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTYB4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3
References: UniProt: Q93088, betaine-homocysteine S-methyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CBH / S-(D-CARBOXYBUTYL)-L-HOMOCYSTEINE


Mass: 235.301 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H17NO4S
#4: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 431 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: PEG 200, sodium citrate, N,N-dimethylglycine, pH 5.20, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
220 mMTris1droppH8.0
35 mMbeta-mercaptoethanol1drop
410 mMDMG1drop
540 %PEG2001drop
60.1 Msodium citrate1droppH5.20
740 %PEG2001reservoir
80.1 Msodium citrate1reservoirpH5.20

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 26, 2001 / Details: Bent conical Si-mirror (Rh coating)
RadiationMonochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.05→100 Å / Num. all: 45962 / Num. obs: 45962 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.88 % / Biso Wilson estimate: 38.9 Å2 / Limit h max: 45 / Limit h min: -53 / Limit k max: 44 / Limit k min: -53 / Limit l max: 43 / Limit l min: 0 / Observed criterion F max: 2569593.7 / Observed criterion F min: 16.3 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 9.3
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 2.37 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 2.46 / Num. unique all: 4569 / Rsym value: 0.289 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 46046 / Redundancy: 2.9 % / Num. measured all: 131321 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1lt7

1lt7


Resolution: 2.05→10 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 0.75 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Residues 326-331 from chain A in this model were generated from the model for chain B using non-crystallographic symmetry operators. Electron density in this region of the map is very poor.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 2317 5.1 %RANDOM
Rwork0.226 ---
all0.236 45626 --
obs0.236 45584 99.9 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 74.3159 Å2 / ksol: 0.41302 e/Å3
Displacement parametersBiso max: 100.27 Å2 / Biso mean: 43.12 Å2 / Biso min: 11.96 Å2
Baniso -1Baniso -2Baniso -3
1--2.24 Å20 Å24.86 Å2
2---6.09 Å20 Å2
3---8.33 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.28 Å
Luzzati d res high-2.05
Refinement stepCycle: LAST / Resolution: 2.05→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5337 0 58 431 5826
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg23.1
X-RAY DIFFRACTIONx_torsion_impr_deg0.99
X-RAY DIFFRACTIONx_mcbond_it1.171.5
X-RAY DIFFRACTIONx_mcangle_it1.852
X-RAY DIFFRACTIONx_scbond_it1.82
X-RAY DIFFRACTIONx_scangle_it2.492.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.05-2.140.3372784.90.29653920.025693567099.6
2.14-2.250.3272995.30.28553670.0195682566699.7
2.25-2.390.3142654.70.26854270.0195698569299.9
2.39-2.580.2943035.30.25253880.01756935691100
2.58-2.830.263025.30.23154070.0155712570999.9
2.83-3.230.2413025.30.22353930.01456965695100
3.23-4.020.2322824.90.20254230.01457065705100
4.02-100.2328650.20454700.0145784575699.5
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / % reflection Rfree: 5 % / Rfactor all: 0.236 / Rfactor Rfree: 0.255 / Rfactor Rwork: 0.225
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg1.426
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shell
*PLUS
Rfactor Rfree: 0.337 / Rfactor Rwork: 0.296

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