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- PDB-4ztx: Neurospora crassa cobalamin-independent methionine synthase compl... -

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Basic information

Entry
Database: PDB / ID: 4ztx
TitleNeurospora crassa cobalamin-independent methionine synthase complexed with Zn2+
ComponentsCobalamin-Independent Methionine synthase
KeywordsTRANSFERASE / homocysteine / methyltetrahydrofolate / tim barrel (alpha/beta barrel) / methionine synthesis / methyltransferase
Function / homology
Function and homology information


: / 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase / 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity / 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
NITRATE ION / 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsWheatley, R.W. / Ng, K.K. / Kapoor, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Arch.Biochem.Biophys. / Year: 2015
Title: Fungal cobalamin-independent methionine synthase: Insights from the model organism, Neurospora crassa.
Authors: Wheatley, R.W. / Ng, K.K. / Kapoor, M.
History
DepositionMay 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Jan 6, 2016Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software
Revision 1.5Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cobalamin-Independent Methionine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9267
Polymers86,4311
Non-polymers4966
Water13,133729
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint0 kcal/mol
Surface area31000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.254, 94.630, 114.907
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cobalamin-Independent Methionine synthase


Mass: 86430.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Neurospora crassa (fungus)
References: UniProt: Q8X1E4, 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 729 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 22% w/v PEG3350, 150 mM potassium nitrate, 1 mM DTT, 20% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.282963 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 27, 2007
RadiationMonochromator: double flat crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282963 Å / Relative weight: 1
ReflectionResolution: 2.1→60 Å / Num. all: 49989 / Num. obs: 49989 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.2 % / Biso Wilson estimate: 26.564 Å2 / Rsym value: 0.064 / Net I/σ(I): 39.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 5.8 / Num. unique all: 4718 / Rsym value: 0.25 / % possible all: 94.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→60 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.058 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.205 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21673 2545 5.1 %RANDOM
Rwork0.16333 ---
all0.16599 47388 --
obs0.16599 47388 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.166 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--1.37 Å20 Å2
3----1.78 Å2
Refinement stepCycle: LAST / Resolution: 2.1→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6089 0 29 729 6847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226259
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0071.9668479
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.435767
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25424.321287
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.331151080
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1311537
X-RAY DIFFRACTIONr_chiral_restr0.0720.2934
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214742
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.59123850
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.532.56223
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8073.52409
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.7714.52256
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 186 -
Rwork0.191 3328 -
obs-3514 94.77 %

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