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- PDB-3qty: Crystal structure of Phosphoribosylaminoimidazole Synthetase from... -

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Basic information

Entry
Database: PDB / ID: 3qty
TitleCrystal structure of Phosphoribosylaminoimidazole Synthetase from Francisella tularensis complexed with pyrophosphate
ComponentsPhosphoribosylaminoimidazole (AIR) synthetase
KeywordsLIGASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta fold
Function / homology
Function and homology information


phosphoribosylformylglycinamidine cyclo-ligase / phosphoribosylformylglycinamidine cyclo-ligase activity / 'de novo' IMP biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / Phosphoribosylformylglycinamidine cyclo-ligase / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain ...Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal domain / Phosphoribosylformylglycinamidine cyclo-ligase / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain / 60s Ribosomal Protein L30; Chain: A; / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / PHOSPHATE ION / PYROPHOSPHATE 2- / Phosphoribosylformylglycinamidine cyclo-ligase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMaltseva, N. / Kim, Y. / Hasseman, J. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of Phosphoribosylaminoimidazole Synthetase from Francisella tularensis complexed with pyrophosphate
Authors: Maltseva, N. / Kim, Y. / Hasseman, J. / Anderson, W.F. / Joachimiak, A.
History
DepositionFeb 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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_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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoribosylaminoimidazole (AIR) synthetase
B: Phosphoribosylaminoimidazole (AIR) synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,77013
Polymers77,4982
Non-polymers1,27211
Water9,656536
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-64 kcal/mol
Surface area27900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.482, 88.721, 112.982
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Phosphoribosylaminoimidazole (AIR) synthetase


Mass: 38748.988 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: SCHU S4 / Gene: FTT_0893, purM / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic
References: UniProt: Q5NGF2, phosphoribosylformylglycinamidine cyclo-ligase

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Non-polymers , 6 types, 547 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H2O7P2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 536 / 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: 2.12 Å3/Da / Density % sol: 41.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M Lithium sulfate, 0.1M Tris pH7.0, 2.0 M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97903 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 18, 2010 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 61612 / Num. obs: 61612 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Biso Wilson estimate: 21.45 Å2 / Rsym value: 0.1 / Net I/σ(I): 12.6
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 3029 / Rsym value: 0.737 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: dev_601)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3M84

3m84


Resolution: 1.8→34.667 Å / SU ML: 0.18 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.53 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.202 3115 5.08 %random
Rwork0.169 ---
all0.171 61302 --
obs0.171 61302 99.37 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.832 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso mean: 28.9 Å2
Baniso -1Baniso -2Baniso -3
1-9.2182 Å2-0 Å2-0 Å2
2---8.2201 Å2-0 Å2
3----0.9981 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.667 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5184 0 72 536 5792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075769
X-RAY DIFFRACTIONf_angle_d1.2287855
X-RAY DIFFRACTIONf_dihedral_angle_d16.1112170
X-RAY DIFFRACTIONf_chiral_restr0.113866
X-RAY DIFFRACTIONf_plane_restr0.0061041
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.8001-1.82830.28161110.23432517262895
1.8283-1.85820.24711450.23242615276099
1.8582-1.89030.26511360.213826322768100
1.8903-1.92470.25671440.212726132757100
1.9247-1.96170.24841350.198325992734100
1.9617-2.00170.22661430.18842627276799
2.0017-2.04520.24951540.183326122766100
2.0452-2.09280.24281410.179725942735100
2.0928-2.14510.21551130.177526562769100
2.1451-2.20310.23921480.17522636278499
2.2031-2.26790.24321310.170126392770100
2.2679-2.34110.20341330.177426522785100
2.3411-2.42480.22221360.171526302766100
2.4248-2.52180.28261280.17732650277899
2.5218-2.63660.19721320.189326472779100
2.6366-2.77550.20851710.190926222793100
2.7755-2.94930.24051600.181226312791100
2.9493-3.17690.18731560.174826722828100
3.1769-3.49630.18821530.152526742827100
3.4963-4.00160.16351370.13727032840100
4.0016-5.03910.13571600.12727342894100
5.0391-34.67310.19331480.17312832298099
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.16420.08030.18010.8303-0.00740.25020.04610.0081-0.00790.1041-0.02790.03650.0090.01330.00470.07890.00570.00770.0406-0.00490.02857.947916.759123.8175
20.7160.39810.30291.27280.30710.37180.0124-0.0157-0.04690.1057-0.03440.05240.0369-0.01430.00560.12920.00360.0030.1413-0.00630.12741.8432-5.14588.1508
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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