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- PDB-1jbw: FPGS-AMPPCP-folate complex -

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Basic information

Entry
Database: PDB / ID: 1jbw
TitleFPGS-AMPPCP-folate complex
ComponentsFOLYLPOLYGLUTAMATE SYNTHASE
KeywordsLIGASE / FPGS folate AMPPCP ternary complex
Function / homology
Function and homology information


tetrahydrofolate synthase / dihydrofolate synthase activity / tetrahydrofolylpolyglutamate synthase activity / one-carbon metabolic process / ATP binding / metal ion binding / cytoplasm
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, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / 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, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / 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
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / 5,10-METHYLENE-6-HYDROFOLIC ACID / Folylpolyglutamate synthase
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSun, X. / Cross, J.A. / Bognar, A.L. / Baker, E.N. / Smith, C.A.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Folate-binding triggers the activation of folylpolyglutamate synthetase.
Authors: Sun, X. / Cross, J.A. / Bognar, A.L. / Baker, E.N. / Smith, C.A.
History
DepositionJun 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_distant_solvent_atoms / pdbx_entry_details ...pdbx_distant_solvent_atoms / pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FOLYLPOLYGLUTAMATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7865
Polymers46,6971
Non-polymers1,0894
Water6,990388
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.1, 45.6, 82.7
Angle α, β, γ (deg.)90, 104.6, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein FOLYLPOLYGLUTAMATE SYNTHASE / FOLYLPOLY-GAMMA-GLUTAMATE SYNTHETASE / FPGS


Mass: 46697.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Plasmid: pCYB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P15925, tetrahydrofolate synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ACQ / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TETRAPHOSPHATE


Mass: 585.188 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19N5O15P4
#4: Chemical ChemComp-TMF / 5,10-METHYLENE-6-HYDROFOLIC ACID


Mass: 455.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21N7O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 40.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 26% PEG1500, 120mM KCl, 20mM Hepes, 2mM 5,10-methylenetetrahydrofolate, 20mM MgCl2, 10mM AMPPCP, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
210 mMAMPPCP1drop
320 mM1dropMgCl2
42 mMmTHF1drop
5120 mM1dropKCl
620 mMHEPES1drop
724-26 %(w/v)PEG15001reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 10, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.85→100 Å / Num. all: 33586 / Num. obs: 33586 / % possible obs: 99.8 % / Redundancy: 7.99 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 19.2
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 3 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 100 Å / Num. measured all: 268516
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JBV

1jbv


Resolution: 1.85→100 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1582 5 %random
Rwork0.195 ---
obs-30135 --
Refinement stepCycle: LAST / Resolution: 1.85→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3143 0 61 388 3592
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.31
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 100 Å / % reflection Rfree: 5 % / Rfactor obs: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS

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