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- PDB-1xdj: Crystal Structure of T. maritima Cobalamin-Independent Methionine... -

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Basic information

Entry
Database: PDB / ID: 1xdj
TitleCrystal Structure of T. maritima Cobalamin-Independent Methionine Synthase complexed with Zn2+ and Homocysteine
Components5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
KeywordsTRANSFERASE / TIM BARREL / HOMOCYSTEINE / METHYLTETRAHYDROFOLATE / ZINC
Function / homology
Function and homology information


5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase / 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity / 'de novo' L-methionine biosynthetic process / methylation / zinc ion binding
Similarity search - Function
Cobalamin-independent methionine synthase / Cobalamin-independent methionine synthase MetE, N-terminal / Cobalamin-independent synthase, N-terminal domain / Cobalamin-independent methionine synthase MetE, C-terminal/archaeal / Cobalamin-independent synthase, Catalytic domain / TIM Barrel - #210 / UROD/MetE-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-AMINO-4-MERCAPTO-BUTYRIC ACID / MESO-ERYTHRITOL / 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsPejchal, R. / Ludwig, M.L.
CitationJournal: Plos Biol. / Year: 2005
Title: Cobalamin-independent methionine synthase (MetE): a face-to-face double barrel that evolved by gene duplication
Authors: Pejchal, R. / Ludwig, M.L.
History
DepositionSep 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
B: 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,11010
Polymers180,2732
Non-polymers8388
Water5,368298
1
A: 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6906
Polymers90,1361
Non-polymers5545
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4204
Polymers90,1361
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)167.053, 159.366, 65.639
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase / Methionine synthase / vitamin-B12 independent isozyme / Cobalamin-independent methionine synthase


Mass: 90136.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: metE / Plasmid: PET-151-D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 STAR(DE3)
References: UniProt: Q9X112, 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase

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Non-polymers , 5 types, 306 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-HCS / 2-AMINO-4-MERCAPTO-BUTYRIC ACID / L-Homocysteine / Homocysteine


Type: L-peptide linking / Mass: 135.185 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO2S
#5: Chemical ChemComp-MRY / MESO-ERYTHRITOL / Erythritol


Mass: 122.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.33 Å3/Da / Density % sol: 49.24 %
Crystal growTemperature: 295 K / Method: vapor batch, under oil / pH: 5.2
Details: PEG 4000, SODIUM ACETATE, AMMONIUM SULFATE, pH 5.2, VAPOR BATCH, UNDER OIL, temperature 295K
Crystal grow
*PLUS
pH: 4.6 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein11
225 %PEG400011
30.2 Mammonium sulfate11
40.1 Msodium acetate11pH4.6
512 %PEG400012
60.2 Mammonium sulfate12
70.1 Msodium acetate12pH4.6

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 5ID-B10.9797
SYNCHROTRONAPS 32-ID20.98
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDDec 5, 2003
MAR CCD 165 mm2CCDNov 16, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.981
ReflectionResolution: 2.2→19.9 Å / Num. all: 89637 / Num. obs: 83276 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 21 Å2
Reflection shellResolution: 2.2→2.34 Å / % possible all: 87.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.9 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 3014807.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1666 2 %RANDOM
Rwork0.227 ---
all0.247 89637 --
obs0.227 83276 92.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.1532 Å2 / ksol: 0.353138 e/Å3
Displacement parametersBiso mean: 25.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.25 Å20 Å20 Å2
2---0.56 Å20 Å2
3---1.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11203 0 44 298 11545
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it2.042
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_scangle_it32.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.316 269 2.1 %
Rwork0.272 12658 -
obs-12658 87.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2HCY_MRY.PARAMHCY_MRY.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5ZNSITE_TRIGBI.PARAMZNSITE_TRIGBI.TOP
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_mcangle_it2.042
X-RAY DIFFRACTIONc_scangle_it32.5

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