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- PDB-1ypx: Crystal Structure of the Putative Vitamin-B12 Independent Methion... -

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Basic information

Entry
Database: PDB / ID: 1ypx
TitleCrystal Structure of the Putative Vitamin-B12 Independent Methionine Synthase from Listeria monocytogenes, Northeast Structural Genomics Target LmR13
Componentsputative vitamin-B12 independent methionine synthase family protein
KeywordsTRANSFERASE / alpha-beta protein / whose fold resembles a TIM-barrel protein / Structural Genomics / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity / methionine biosynthetic process / zinc ion binding
Similarity search - Function
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
PHOSPHATE ION / Lmo0845 protein
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsForouhar, F. / Chen, Y. / Benach, J. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of Putative Vitamin-B12 Independent Methionine Synthase from Listeria monocytogenes, Northeast Structural Genomics Target LmR13
Authors: Forouhar, F. / Chen, Y. / Benach, J. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJan 31, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: putative vitamin-B12 independent methionine synthase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2102
Polymers43,1151
Non-polymers951
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.109, 139.109, 38.535
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41

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Components

#1: Protein putative vitamin-B12 independent methionine synthase family protein


Mass: 43114.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: 985330 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q8Y8Q1
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.2 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100mM sodium acetate trihydrate, 30% PEG 2K, 200mM ammonium phosphate, 5mM DTT, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 21, 2004 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 21647 / Num. obs: 21647 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.45 % / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.037 / Net I/σ(I): 19.57
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 4.65 / Num. unique all: 2166 / Rsym value: 0.256 / % possible all: 97.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→29.64 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 637961.86 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.308 1786 9.4 %RANDOM
Rwork0.233 ---
all0.239 21647 --
obs0.233 18969 85.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.6332 Å2 / ksol: 0.301106 e/Å3
Displacement parametersBiso mean: 62.3 Å2
Baniso -1Baniso -2Baniso -3
1--11.19 Å20 Å20 Å2
2---11.19 Å20 Å2
3---22.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2566 0 5 56 2627
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.397 242 10 %
Rwork0.293 2183 -
obs-2183 65.1 %

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