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- PDB-2zw2: Crystal Structure of Formylglycinamide Ribonucleotide Amidotransf... -

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Basic information

Entry
Database: PDB / ID: 2zw2
TitleCrystal Structure of Formylglycinamide Ribonucleotide Amidotransferase III from SULFOLOBUS TOKODAII (STPURS)
ComponentsPutative uncharacterized protein STS178
KeywordsLIGASE / Purine metabolism
Function / homology
Function and homology information


phosphoribosylformylglycinamidine synthase / phosphoribosylformylglycinamidine synthase activity / 'de novo' IMP biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Mth169; Chain: A , / Phosphoribosylformylglycinamidine synthase subunit PurS / Phosphoribosylformylglycinamidine synthase subunit PurS / Phosphoribosylformylglycinamidine (FGAM) synthase / Phosphoribosylformylglycinamidine synthase subunit PurS-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoribosylformylglycinamidine synthase subunit PurS / :
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSuzuki, S. / Tamura, S. / Okada, K. / Baba, S. / Kumasaka, T. / Nakagawa, N. / Masui, R. / Kuramitsu, S. / Sampei, G. / Kawai, G.
CitationJournal: To be Published
Title: Crystal Structure of Formylglycinamide Ribonucleotide Amidotransferase III from SULFOLOBUS TOKODAII (STPURS)
Authors: Suzuki, S. / Tamura, S. / Okada, K. / Baba, S. / Kumasaka, T. / Nakagawa, N. / Masui, R. / Kuramitsu, S. / Sampei, G. / Kawai, G.
History
DepositionNov 27, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein STS178
B: Putative uncharacterized protein STS178
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7114
Polymers21,5272
Non-polymers1842
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-23 kcal/mol
Surface area9750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.821, 68.390, 68.403
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 Putative uncharacterized protein STS178 / Formylglycinamide Ribonucleotide Amidotransferase III / Phosphoribosylformylglycinamidine synthase ...Formylglycinamide Ribonucleotide Amidotransferase III / Phosphoribosylformylglycinamidine synthase III / PurS / STS178


Mass: 10763.329 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: 7 / Gene: purS / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta gami (DE3)
References: UniProt: Q970V8, UniProt: F9VNF4*PLUS, phosphoribosylformylglycinamidine synthase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 1.95 Å3/Da / Density % sol: 36.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES sodium pH7.5, 0.8M potassium sodium tartrate tetrahydrate, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 30, 2008
RadiationMonochromator: Fixed exit Si 111 double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 24008 / Num. obs: 24008 / % possible obs: 97.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 17.4
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1925 / % possible all: 79.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VQ3

1vq3


Resolution: 1.55→24.74 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 315431.83 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2341 9.9 %RANDOM
Rwork0.212 ---
obs0.212 23650 95.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.154 Å2 / ksol: 0.408065 e/Å3
Displacement parametersBiso mean: 21.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.66 Å20 Å20 Å2
2--1.34 Å20 Å2
3---1.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.55→24.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1404 0 12 200 1616
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.55→1.65 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 275 9.6 %
Rwork0.267 2597 -
obs--69.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3gol.paramgol.top

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