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- PDB-2gca: apo form of L. casei FPGS -

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Basic information

Entry
Database: PDB / ID: 2gca
Titleapo form of L. casei FPGS
ComponentsFolylpolyglutamate synthase
KeywordsLIGASE / ATPase / P-loop enzyme / apo form
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: 2.4 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 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 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: Folylpolyglutamate synthase


Theoretical massNumber of molelcules
Total (without water)46,6401
Polymers46,6401
Non-polymers00
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.070, 45.940, 85.380
Angle α, β, γ (deg.)90.00, 107.89, 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: 46639.988 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 40 mM acetate buffer, 4% PEG4000, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationMonochromator: Graphite monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 13391 / Num. obs: 13391 / % possible obs: 84.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.096 / Net I/σ(I): 7.3
Reflection shellResolution: 2.4→2.48 Å / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 2.1 / % possible all: 88.4

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Processing

Software
NameVersionClassification
ROTAVATAdata reduction
AMoREphasing
CNS0.9refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→20 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2484 577 random 5%
Rwork0.1741 --
obs-10465 -
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3127 0 0 201 3328
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2

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