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

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Basic information

Entry
Database: PDB / ID: 3ppg
TitleCrystal structure of the Candida albicans methionine synthase by surface entropy reduction, alanine variant with 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: 1.98 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)88,2542
Polymers88,1891
Non-polymers651
Water9,026501
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.194, 99.217, 100.823
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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 2.25 Å3/Da / Density % sol: 45.44 %
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: 5.0.3 / Wavelength: 0.9765 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2010 / 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: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. all: 54885 / Num. obs: 54885 / % possible obs: 100 % / Redundancy: 10 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.98-2.01100.6291100
2.01-2.05100.5181100
2.05-2.09100.471100
2.09-2.1310.10.3771100
2.13-2.1810.10.3331100
2.18-2.2310.10.2941100
2.23-2.2910.10.2681100
2.29-2.3510.20.2161100
2.35-2.4210.20.1891100
2.42-2.4910.20.1671100
2.49-2.5810.20.1441100
2.58-2.6910.20.1261100
2.69-2.8110.20.111100
2.81-2.9610.20.0931100
2.96-3.1410.20.0811100
3.14-3.3910.10.0751100
3.39-3.739.70.0731100
3.73-4.269.50.0651100
4.26-5.379.60.0471100
5.37-509.60.032199.9

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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: 1.98→49.609 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.22 / σ(F): 0 / Phase error: 21.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2201 2682 5.03 %
Rwork0.178 --
obs0.1801 53282 97 %
all-54885 -
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.335 Å2 / ksol: 0.283 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.6256 Å2-0 Å20 Å2
2---3.769 Å2-0 Å2
3---6.3946 Å2
Refinement stepCycle: LAST / Resolution: 1.98→49.609 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5514 0 1 501 6016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075626
X-RAY DIFFRACTIONf_angle_d0.9827670
X-RAY DIFFRACTIONf_dihedral_angle_d12.2331975
X-RAY DIFFRACTIONf_chiral_restr0.066893
X-RAY DIFFRACTIONf_plane_restr0.004999
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.01170.24721240.20892353X-RAY DIFFRACTION88
2.0117-2.05040.25221390.19692530X-RAY DIFFRACTION93
2.0504-2.09230.27041460.19032547X-RAY DIFFRACTION94
2.0923-2.13780.2591330.18142605X-RAY DIFFRACTION96
2.1378-2.18750.21651200.17162584X-RAY DIFFRACTION96
2.1875-2.24220.23331380.16732594X-RAY DIFFRACTION95
2.2422-2.30280.20781520.1682564X-RAY DIFFRACTION96
2.3028-2.37060.241430.1662636X-RAY DIFFRACTION97
2.3706-2.44710.23171380.16982648X-RAY DIFFRACTION97
2.4471-2.53460.24431300.17832680X-RAY DIFFRACTION98
2.5346-2.6360.2451460.17962661X-RAY DIFFRACTION98
2.636-2.7560.23651340.18982724X-RAY DIFFRACTION99
2.756-2.90130.27851240.20042714X-RAY DIFFRACTION99
2.9013-3.0830.24451410.19662746X-RAY DIFFRACTION99
3.083-3.3210.24841400.18852740X-RAY DIFFRACTION100
3.321-3.65510.21041390.1812779X-RAY DIFFRACTION100
3.6551-4.18380.18691620.16082766X-RAY DIFFRACTION100
4.1838-5.27020.16371630.14772802X-RAY DIFFRACTION100
5.2702-49.62410.22091700.19162927X-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)
11.07750.2161-0.31711.513-0.28150.7454-0.03220.27360.2125-0.41840.07530.1576-0.1094-0.0449-0.02210.24710.0147-0.05610.14870.03050.1538-8.0843-16.210311.5076
21.02450.0232-0.19391.9234-0.07011.0909-0.01120.0277-0.0425-0.0675-0.0438-0.04890.08260.02780.04620.1090.0215-0.00130.11340.00110.1138-4.5214-29.04925.4587
30.559-0.5797-0.24540.95110.19850.33420.08150.13660.20240.0337-0.14810.2617-0.13120.22280.00520.20360.0206-0.00460.32740.09130.2878-39.2651-7.20439.4093
42.1655-0.0571-0.03130.2640.3910.58250.17530.65530.3432-0.37130.0649-0.1911-0.30730.0815-0.21490.33310.07680.08550.35790.18210.5112-28.07689.583126.9901
51.04460.0663-0.30780.67160.11310.11390.0482-0.01140.2476-0.06370.04280.0608-0.0491-0.106-0.09380.18420.04110.01830.19880.00580.2318-25.2458-4.762135.8271
61.8081-0.86160.24170.68230.16270.33340.0219-0.272-0.12340.02470.1609-0.4523-0.0986-0.0491-0.17480.16890.00150.09610.1778-0.05220.3634-26.594-25.436234.497
73.816-1.16081.26292.7602-0.08420.52670.41790.9962-0.3967-0.8341-0.2490.615-0.00420.1383-0.05720.42750.1497-0.14140.5087-0.07080.2848-43.7329-9.033123.816
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:140)
2X-RAY DIFFRACTION2(chain A and resid 141:399)
3X-RAY DIFFRACTION3(chain A and resid 400:451)
4X-RAY DIFFRACTION4(chain A and resid 452:511)
5X-RAY DIFFRACTION5(chain A and resid 512:619)
6X-RAY DIFFRACTION6(chain A and resid 620:638)
7X-RAY DIFFRACTION7(chain A and resid 639:767)

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