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- PDB-1w7k: E.coli FolC in complex with ADP, without folate substrate -

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Basic information

Entry
Database: PDB / ID: 1w7k
TitleE.coli FolC in complex with ADP, without folate substrate
ComponentsFOLC BIFUNCTIONAL PROTEIN
KeywordsSYNTHASE / FOLC / DHFS / DIHYDROFOLATE SYNTHASE / ATP-BINDING / FOLATE BIOSYNTHESIS / LIGASE / MULTIFUNCTIONAL ENZYME
Function / homology
Function and homology information


dihydrofolate synthase / dihydrofolate biosynthetic process / tetrahydrofolylpolyglutamate biosynthetic process / tetrahydrofolate synthase / dihydrofolate synthase activity / folic acid-containing compound biosynthetic process / tetrahydrofolylpolyglutamate synthase activity / 10-formyltetrahydrofolate biosynthetic process / folic acid biosynthetic process / guanosine tetraphosphate binding ...dihydrofolate synthase / dihydrofolate biosynthetic process / tetrahydrofolylpolyglutamate biosynthetic process / tetrahydrofolate synthase / dihydrofolate synthase activity / folic acid-containing compound biosynthetic process / tetrahydrofolylpolyglutamate synthase activity / 10-formyltetrahydrofolate biosynthetic process / folic acid biosynthetic process / guanosine tetraphosphate binding / 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
ADENOSINE-5'-DIPHOSPHATE / Dihydrofolate synthase/folylpolyglutamate synthase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMathieu, M. / Debousker, G. / Vincent, S. / Viviani, F. / Bamas-Jacques, N. / Mikol, V.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Escherichia Coli Folc Structure Reveals an Unexpected Dihydrofolate Binding Site Providing an Attractive Target for Anti-Microbial Therapy
Authors: Mathieu, M. / Debousker, G. / Vincent, S. / Viviani, F. / Bamas-Jacques, N. / Mikol, V.
History
DepositionSep 6, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 / _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_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: FOLC BIFUNCTIONAL PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0715
Polymers45,5001
Non-polymers5724
Water7,837435
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)66.112, 81.602, 93.673
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 FOLC BIFUNCTIONAL PROTEIN / FOLYLPOLYGLUTAMATE SYNTHASE / FOLYLPOLY-GAMMA-GLUTAMATE SYNTHETASE / FPGS / DIHYDROFOLATE SYNTHASE


Mass: 45499.543 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PVRC1432 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): PVRC 1432 / References: UniProt: P08192, dihydrofolate synthase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: ATP + DIHYDROPTERATE + L-GLUTAMATE = ADP + PHOSPHATE + DIHYDROFOLATE.

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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: 2.78 Å3/Da / Density % sol: 55.7 %
Crystal growpH: 8.7
Details: 1.5 M AMMONIUM SULFATE 5 MM DTT 50 MM BICINE PH 8.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MACSCIENCE DIP2000 / Detector: IMAGE PLATE / Date: Sep 19, 2000 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→31.2 Å / Num. obs: 29894 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.8
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameClassification
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W78

1w78


Resolution: 2.1→31.16 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1477 5 %RANDOM
Rwork0.177 ---
obs-28893 --
Refinement stepCycle: LAST / Resolution: 2.1→31.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3113 0 34 435 3582

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