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- PDB-1fgs: FOLYLPOLYGLUTAMATE SYNTHETASE FROM LACTOBACILLUS CASEI -

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Basic information

Entry
Database: PDB / ID: 1fgs
TitleFOLYLPOLYGLUTAMATE SYNTHETASE FROM LACTOBACILLUS CASEI
ComponentsFOLYLPOLYGLUTAMATE SYNTHETASE
KeywordsSYNTHETASE / LIGASE
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
PYROPHOSPHATE 2- / Folylpolyglutamate synthase
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.4 Å
AuthorsSun, X. / Bognar, A. / Baker, E. / Smith, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Structural homologies with ATP- and folate-binding enzymes in the crystal structure of folylpolyglutamate synthetase.
Authors: Sun, X. / Bognar, A.L. / Baker, E.N. / Smith, C.A.
History
DepositionApr 29, 1998Processing site: BNL
Revision 1.0May 4, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: 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_struct_conn_angle / software / 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_asym_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_asym_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 / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_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: FOLYLPOLYGLUTAMATE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8543
Polymers46,6541
Non-polymers2002
Water3,045169
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.000, 46.100, 84.900
Angle α, β, γ (deg.)90.00, 107.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FOLYLPOLYGLUTAMATE SYNTHETASE / FPGS


Mass: 46654.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P15925, tetrahydrofolate synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growpH: 5.3 / Details: pH 5.3
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 mMacetate1reservoir
25 mMMgATP1reservoir
34 %PEG40001reservoir
45 mg/mlFPGS1drop
510 mMMgATP1drop

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Data collection

DiffractionMean temperature: 285 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 20, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 15725 / % possible obs: 100 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 9.5
Reflection shellResolution: 2.4→2.5 Å / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 2.2 / % possible all: 100
Reflection
*PLUS
Num. measured all: 39117

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Processing

Software
NameClassification
MLPHAREphasing
TNTrefinement
DENZOdata reduction
Agrovatadata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.4→15 Å / Num. reflection all: 16120 / Num. reflection obs: 15311 / Stereochemistry target values: ENGH AND HUBER
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2988 0 10 169 3167
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.008
X-RAY DIFFRACTIONt_angle_deg1.46
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Num. reflection Rfree: 809 / % reflection Rfree: 5 % / Rfactor obs: 0.196 / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.196 / Lowest resolution: 15 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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