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- PDB-6jt9: Crystal Structure of D464A mutant of FGAM Synthetase -

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Basic information

Entry
Database: PDB / ID: 6jt9
TitleCrystal Structure of D464A mutant of FGAM Synthetase
ComponentsPhosphoribosylformylglycinamidine synthase
KeywordsBIOSYNTHETIC PROTEIN / FGAM Synthetase
Function / homology
Function and homology information


phosphoribosylformylglycinamidine synthase / phosphoribosylformylglycinamidine synthase activity / purine nucleotide biosynthetic process / glutamine metabolic process / 'de novo' IMP biosynthetic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Phosphoribosylformylglycinamidine synthase PurL / Phosphoribosylformylglycinamidine synthase, N-terminal / : / Formylglycinamide ribonucleotide amidotransferase N-terminal / FGAR-AT PurM_N-like domain / CobB/CobQ-like glutamine amidotransferase domain / CobB/CobQ-like glutamine amidotransferase domain / Phosphoribosylformylglycinamidine synthase, linker domain / Formylglycinamide ribonucleotide amidotransferase linker domain / Phosphoribosylformylglycinamidine synthase subunit PurS-like superfamily ...Phosphoribosylformylglycinamidine synthase PurL / Phosphoribosylformylglycinamidine synthase, N-terminal / : / Formylglycinamide ribonucleotide amidotransferase N-terminal / FGAR-AT PurM_N-like domain / CobB/CobQ-like glutamine amidotransferase domain / CobB/CobQ-like glutamine amidotransferase domain / Phosphoribosylformylglycinamidine synthase, linker domain / Formylglycinamide ribonucleotide amidotransferase linker domain / Phosphoribosylformylglycinamidine synthase subunit PurS-like superfamily / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase-like
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Phosphoribosylformylglycinamidine synthase / Phosphoribosylformylglycinamidine synthase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSharma, N. / Ahalawat, N. / Sandhu, P. / Mondal, J. / Anand, R.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (India)DST/INT/SOUTH AFRICA/P-04/2014 India
CitationJournal: Sci Adv / Year: 2020
Title: Role of allosteric switches and adaptor domains in long-distance cross-talk and transient tunnel formation.
Authors: Sharma, N. / Ahalawat, N. / Sandhu, P. / Strauss, E. / Mondal, J. / Anand, R.
History
DepositionApr 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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_conn_type
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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _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_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_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoribosylformylglycinamidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,16328
Polymers142,6671
Non-polymers2,49627
Water15,403855
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-15 kcal/mol
Surface area41430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.461, 146.461, 141.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phosphoribosylformylglycinamidine synthase / FGAMS / Formylglycinamide ribonucleotide amidotransferase / FGAR-AT


Mass: 142666.531 Da / Num. of mol.: 1 / Mutation: D464A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: purL, C2273_06610, DD95_10355 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0D6F9Y3, UniProt: P74881*PLUS, phosphoribosylformylglycinamidine synthase

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Non-polymers , 6 types, 882 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: 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
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 855 / 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: 3.07 Å3/Da / Density % sol: 59.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2M Ammonium Sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 100187 / % possible obs: 100 % / Redundancy: 5.6 % / Rpim(I) all: 0.048 / Net I/σ(I): 24.7
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 4987 / Rpim(I) all: 0.185

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T3T

1t3t


Resolution: 2.1→32.52 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.319 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.138 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18891 5004 5 %RANDOM
Rwork0.14534 ---
obs0.14753 95120 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.925 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.1→32.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9878 0 141 855 10874
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.01910408
X-RAY DIFFRACTIONr_bond_other_d0.0020.029780
X-RAY DIFFRACTIONr_angle_refined_deg1.9441.96414167
X-RAY DIFFRACTIONr_angle_other_deg1.07322467
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.90251336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63724.045492
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.985151671
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0291579
X-RAY DIFFRACTIONr_chiral_restr0.120.21564
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02112022
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022420
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4572.5975221
X-RAY DIFFRACTIONr_mcbond_other2.4562.5975220
X-RAY DIFFRACTIONr_mcangle_it3.4483.8796547
X-RAY DIFFRACTIONr_mcangle_other3.4483.8796548
X-RAY DIFFRACTIONr_scbond_it3.4862.945187
X-RAY DIFFRACTIONr_scbond_other3.4862.945187
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1074.287604
X-RAY DIFFRACTIONr_long_range_B_refined8.62421.40112519
X-RAY DIFFRACTIONr_long_range_B_other8.62321.40312520
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.222 366 -
Rwork0.168 7002 -
obs--99.92 %

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