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- PDB-1lt7: Oxidized Homo sapiens betaine-homocysteine S-methyltransferase in... -

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Basic information

Entry
Database: PDB / ID: 1lt7
TitleOxidized Homo sapiens betaine-homocysteine S-methyltransferase in complex with four Sm(III) ions
ComponentsBETAINE-HOMOCYSTEINE METHYLTRANSFERASE
KeywordsTRANSFERASE / homocysteine metabolism / homocysteinemia / thiol alkyl transfer
Function / homology
Function and homology information


: / 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 ...: / 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
CITRIC ACID / SAMARIUM (III) ION / Betaine--homocysteine S-methyltransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 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: Derived calculations / 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_asym_id / _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.ptnr3_auth_asym_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.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.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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water5,368298
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
Buried area16140 Å2
ΔGint-65 kcal/mol
Surface area45660 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)109.990, 90.085, 89.085
Angle α, β, γ (deg.)90.00, 122.10, 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-SM / SAMARIUM (III) ION


Mass: 150.360 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Sm
#3: Chemical ChemComp-CIT / CITRIC ACID


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


Mass: 18.015 Da / Num. of mol.: 298 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.08 Å3/Da / Density % sol: 40.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: PEG 200, sodium citrate, N,N-dimethylglycine, samarium (III) acetate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 5.2
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: 5ID-B / Wavelength: 1.845, 1.746
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 12, 2002
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.8451
21.7461
ReflectionResolution: 2.15→100 Å / Num. all: 78638 / Num. obs: 78638 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.88 % / Biso Wilson estimate: 40.2 Å2 / Limit h max: 51 / Limit h min: 0 / Limit k max: 41 / Limit k min: 0 / Limit l max: 34 / Limit l min: -41 / Observed criterion F max: 324855.27 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 17.3
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 1.82 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 3.41 / Num. unique all: 7838 / Rsym value: 0.213 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 50 Å / Num. obs: 40062 / Redundancy: 3.7 % / Num. measured all: 148174
Reflection shell
*PLUS
% possible obs: 99.9 % / Mean I/σ(I) obs: 3.4

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.15→9.99 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 0.3 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 7403 9.9 %RANDOM
Rwork0.203 ---
all0.218 77987 --
obs0.218 75110 96.3 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 100.343 Å2 / ksol: 0.491514 e/Å3
Displacement parametersBiso max: 100.17 Å2 / Biso mean: 36.79 Å2 / Biso min: 11.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.19 Å20 Å22.07 Å2
2---2.63 Å20 Å2
3---4.82 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
nonpolymerX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.17 Å
Luzzati d res high-2.15
Refinement stepCycle: LAST / Resolution: 2.15→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4818 0 30 298 5146
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_torsion_deg23.1
X-RAY DIFFRACTIONx_torsion_impr_deg1.17
X-RAY DIFFRACTIONx_mcbond_it1.461.5
X-RAY DIFFRACTIONx_mcangle_it2.292
X-RAY DIFFRACTIONx_scbond_it2.252
X-RAY DIFFRACTIONx_scangle_it3.172.5
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 (%)
2.15-2.250.2958699.90.24378870.019704875690.2
2.25-2.360.288449.30.22182340.019772907892.9
2.36-2.510.26693610.10.20283450.0099779928194.9
2.51-2.70.2459289.90.19184780.0089759940696.4
2.7-2.970.256949100.19485880.0089769953797.6
2.97-3.380.2359289.70.19186800.0089758960898.5
3.38-4.20.22898910.20.18787340.0079774972399.5
4.2-9.990.2539609.90.2287610.0089742972199.8
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2my_ion.parammy_ion.top
X-RAY DIFFRACTION3water.paramwater.top
X-RAY DIFFRACTION4citrate.cns.paramcitrate.cns.top
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.248
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg1.802
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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