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- PDB-2gc6: S73A mutant of L. casei FPGS -

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Basic information

Entry
Database: PDB / ID: 2gc6
TitleS73A mutant of L. casei FPGS
ComponentsFolylpolyglutamate synthase
KeywordsLIGASE / ATPase / P-loop / site-directed mutant
Function / homology
Function and homology information


tetrahydrofolate synthase / tetrahydrofolylpolyglutamate synthase activity / one-carbon metabolic process / ATP binding / metal ion binding
Similarity search - Function
Folylpolyglutamate synthase signature 2. / Folylpolyglutamate synthetase / Folylpolyglutamate synthase signature 1. / Folylpolyglutamate synthetase, conserved site / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase family, glutamate ligase domain / Mur ligase, C-terminal domain superfamily / Mur ligase, central ...Folylpolyglutamate synthase signature 2. / Folylpolyglutamate synthetase / Folylpolyglutamate synthase signature 1. / Folylpolyglutamate synthetase, conserved site / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase family, glutamate ligase domain / Mur ligase, C-terminal domain superfamily / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Protein-Tyrosine Phosphatase; Chain A / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Folylpolyglutamate synthase
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSmith, C.A. / Cross, J.A. / Bognar, A.L. / Sun, X.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Mutation of Gly51 to serine in the P-loop of Lactobacillus casei folylpolyglutamate synthetase abolishes activity by altering the conformation of two adjacent loops.
Authors: Smith, C.A. / Cross, J.A. / Bognar, A.L. / Sun, X.
History
DepositionMar 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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: Folylpolyglutamate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7632
Polymers46,6671
Non-polymers961
Water4,936274
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.120, 45.860, 84.270
Angle α, β, γ (deg.)90.00, 106.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Folylpolyglutamate synthase / / Folylpoly-gamma-glutamate synthetase / FPGS / Tetrahydrofolate synthase / ...Folylpoly-gamma-glutamate synthetase / FPGS / Tetrahydrofolate synthase / Tetrahydrofolylpolyglutamate synthase


Mass: 46666.988 Da / Num. of mol.: 1 / Mutation: S73A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Gene: fgs / Production host: Escherichia coli (E. coli) / References: UniProt: P15925, tetrahydrofolate synthase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.1 Å3/Da / Density % sol: 41.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 50 mM acetate and 16-24% PEG4000, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: Osmic optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 29157 / Num. obs: 29157 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.06 / Net I/σ(I): 21
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.292 / Mean I/σ(I) obs: 3.8 / % possible all: 93.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.91 / SU B: 3.338 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.163 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1380 4.9 %RANDOM 5%
Rwork0.191 ---
obs0.193 26921 97.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.172 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3112 0 5 274 3391
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223182
X-RAY DIFFRACTIONr_angle_refined_deg1.371.9494346
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9175403
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.22523.971136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37115493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4291520
X-RAY DIFFRACTIONr_chiral_restr0.0940.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022408
X-RAY DIFFRACTIONr_nbd_refined0.2020.21367
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22201
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2178
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1420.214
X-RAY DIFFRACTIONr_mcbond_it0.8671.52082
X-RAY DIFFRACTIONr_mcangle_it1.36623265
X-RAY DIFFRACTIONr_scbond_it2.01231246
X-RAY DIFFRACTIONr_scangle_it3.1684.51081
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 55 -
Rwork0.223 1346 -
obs--92.11 %

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