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- PDB-3ppf: Crystal structure of the Candida albicans methionine synthase by ... -

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Basic information

Entry
Database: PDB / ID: 3ppf
TitleCrystal structure of the Candida albicans methionine synthase by surface entropy reduction, alanine variant without zinc
Components5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
KeywordsTRANSFERASE / cobalamin-independent / Surface entropy reduction / Methyltransferase / Metalloproteinase
Function / homology
Function and homology information


L-methionine biosynthetic process from homoserine via O-acetyl-L-homoserine and cystathionine / : / 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase / 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity / fungal biofilm matrix / hyphal cell wall / adenine biosynthetic process / methionine synthase activity / methionine metabolic process / 'de novo' L-methionine biosynthetic process ...L-methionine biosynthetic process from homoserine via O-acetyl-L-homoserine and cystathionine / : / 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase / 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity / fungal biofilm matrix / hyphal cell wall / adenine biosynthetic process / methionine synthase activity / methionine metabolic process / 'de novo' L-methionine biosynthetic process / fungal-type cell wall / methionine biosynthetic process / cellular response to heat / methylation / cell surface / zinc ion binding / extracellular region / nucleus / cytosol
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
5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsUbhi, D. / Kavanagh, K. / Monzingo, A.F. / Robertus, J.D.
CitationJournal: Arch.Biochem.Biophys. / Year: 2011
Title: Structure of Candida albicans methionine synthase determined by employing surface residue mutagenesis.
Authors: Ubhi, D. / Kavanagh, K.L. / Monzingo, A.F. / Robertus, J.D.
History
DepositionNov 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase


Theoretical massNumber of molelcules
Total (without water)88,1891
Polymers88,1891
Non-polymers00
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.862, 98.814, 100.750
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 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase / Cobalamin-independent methionine synthase / Methionine synthase / vitamin-B12 independent isozyme


Mass: 88188.961 Da / Num. of mol.: 1 / Mutation: K103A, K104A, E107A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Strain: BWP17 / Gene: CaO19.10083, CaO19.2551, MET6 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P82610, 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.23 Å3/Da / Density % sol: 44.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 50 mM NaI, 27% (w/v) PEG 3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2009 / Details: Asymmetric cut single crystal Si (220)
RadiationMonochromator: Asymmetric cut single crystal Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 35447 / Num. obs: 35447 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.3-2.346.20.545199.3
2.34-2.386.20.41199.6
2.38-2.436.20.382199.8
2.43-2.486.20.357199.8
2.48-2.536.30.321199.8
2.53-2.596.30.275199.8
2.59-2.666.30.2671100
2.66-2.736.30.244199.9
2.73-2.816.40.2021100
2.81-2.96.50.1711100
2.9-36.60.1441100
3-3.126.60.1161100
3.12-3.266.60.091100
3.26-3.446.60.081100
3.44-3.656.50.0711100
3.65-3.936.40.063199.8
3.93-4.336.50.0431100
4.33-4.956.50.0371100
4.95-6.246.40.038199.8
6.24-505.90.037199.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3PPC

3ppc


Resolution: 2.3→49.407 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.3 / σ(F): 0 / Phase error: 24.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2532 1629 5.03 %
Rwork0.1806 --
obs0.1844 32385 93.14 %
all-35447 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.813 Å2 / ksol: 0.317 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.2925 Å2-0 Å20 Å2
2---5.3837 Å2-0 Å2
3---4.0913 Å2
Refinement stepCycle: LAST / Resolution: 2.3→49.407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5423 0 0 400 5823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075529
X-RAY DIFFRACTIONf_angle_d1.0477532
X-RAY DIFFRACTIONf_dihedral_angle_d12.5681948
X-RAY DIFFRACTIONf_chiral_restr0.067879
X-RAY DIFFRACTIONf_plane_restr0.005984
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.36770.25691130.1942331X-RAY DIFFRACTION86
2.3677-2.44420.29631370.18372379X-RAY DIFFRACTION88
2.4442-2.53150.26351050.18472452X-RAY DIFFRACTION90
2.5315-2.63290.26271130.1712413X-RAY DIFFRACTION88
2.6329-2.75270.26551340.19122425X-RAY DIFFRACTION89
2.7527-2.89780.31331380.20092422X-RAY DIFFRACTION89
2.8978-3.07930.29721300.2082541X-RAY DIFFRACTION92
3.0793-3.3170.28771450.20212699X-RAY DIFFRACTION99
3.317-3.65070.30181570.18822736X-RAY DIFFRACTION99
3.6507-4.17880.26191290.15892693X-RAY DIFFRACTION97
4.1788-5.26390.17531620.13982755X-RAY DIFFRACTION99
5.2639-49.41840.21331660.19412910X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.46970.0788-0.20251.1342-0.11530.2602-0.03750.15130.048-0.36770.07030.0741-0.02130.0032-0.03130.15930.0037-0.03080.06430.02820.0663-7.8461-16.623810.7369
20.3618-0.1309-0.17331.102-0.39980.5448-0.0175-0.0214-0.0432-0.0138-0.0211-0.0040.09120.03050.02620.05260.01040.00770.0502-0.00290.0446-4.3978-28.93825.997
30.4118-0.48370.13990.73170.00270.21260.13590.1818-0.00510.0062-0.02960.2323-0.0295-0.0241-0.09510.13220.01540.06790.2910.10730.1931-39.0248-7.449239.9668
40.54520.0746-0.12790.31730.39090.77440.13340.34970.3146-0.07380.1680.0891-0.14480.0626-0.13330.19160.03550.08310.22050.16550.2799-26.84718.650228.0758
50.58060.4783-0.27050.389-0.23040.17630.04780.0980.04040.02670.01350.1348-0.0408-0.0918-0.04250.06360.04060.02930.07650.01760.0975-25.4928-4.815935.4859
60.27030.2333-0.11660.6817-0.24910.1992-0.0704-0.0478-0.1762-0.02410.0771-0.036-0.013-0.0794-0.02550.0544-0.00740.06340.08710.02840.1525-32.2834-18.144637.4278
72.77640.84910.42432.49311.13230.5181-0.03060.9105-0.3161-0.9115-0.01470.19360.15750.05130.04670.4640.0741-0.10810.4518-0.02610.1688-44.1499-9.914521.1775
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:147)
2X-RAY DIFFRACTION2(chain A and resid 148:399)
3X-RAY DIFFRACTION3(chain A and resid 400:450)
4X-RAY DIFFRACTION4(chain A and resid 451:516)
5X-RAY DIFFRACTION5(chain A and resid 517:619)
6X-RAY DIFFRACTION6(chain A and resid 620:654)
7X-RAY DIFFRACTION7(chain A and resid 655:764)

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