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- PDB-2yw2: Crystal structure of GAR synthetase from Aquifex aeolicus in comp... -

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Basic information

Entry
Database: PDB / ID: 2yw2
TitleCrystal structure of GAR synthetase from Aquifex aeolicus in complex with ATP
ComponentsPhosphoribosylamine--glycine ligase
KeywordsLIGASE / Glycinamide ribonucleotide synthetase / GAR synthetase / ATP binding / Purine nucleotide biosynthetic pathway / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


purine nucleobase biosynthetic process / phosphoribosylamine-glycine ligase / phosphoribosylamine-glycine ligase activity / 'de novo' IMP biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Phosphoribosylglycinamide synthetase, C-terminal domain / Glycinamide Ribonucleotide Synthetase; Chain A, domain 4 / Phosphoribosylglycinamide synthetase / Phosphoribosylglycinamide synthetase, conserved site / Phosphoribosylglycinamide synthetase, C-domain / Phosphoribosylglycinamide synthetase, N-terminal / Phosphoribosylglycinamide synthetase, C-domain superfamily / Phosphoribosylglycinamide synthetase, C domain / Phosphoribosylglycinamide synthetase, N domain / Phosphoribosylglycinamide synthetase signature. ...Phosphoribosylglycinamide synthetase, C-terminal domain / Glycinamide Ribonucleotide Synthetase; Chain A, domain 4 / Phosphoribosylglycinamide synthetase / Phosphoribosylglycinamide synthetase, conserved site / Phosphoribosylglycinamide synthetase, C-domain / Phosphoribosylglycinamide synthetase, N-terminal / Phosphoribosylglycinamide synthetase, C-domain superfamily / Phosphoribosylglycinamide synthetase, C domain / Phosphoribosylglycinamide synthetase, N domain / Phosphoribosylglycinamide synthetase signature. / Phosphoribosylglycinamide synthetase, C domain / Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain / Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain / Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain / Rossmann fold - #20 / ATP-grasp fold, A domain / Rudiment single hybrid motif / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Alpha-Beta Complex / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / PHOSPHATE ION / Phosphoribosylamine--glycine ligase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBaba, S. / Kanagawa, M. / Kuramitsu, S. / Yokoyama, S. / Kawai, G. / Sampei, G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Biochem. / Year: 2010
Title: Crystal structures of glycinamide ribonucleotide synthetase, PurD, from thermophilic eubacteria
Authors: Sampei, G. / Baba, S. / Kanagawa, M. / Yanai, H. / Ishii, T. / Kawai, H. / Fukai, Y. / Ebihara, A. / Nakagawa, N. / Kawai, G.
History
DepositionApr 19, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoribosylamine--glycine ligase
B: Phosphoribosylamine--glycine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2056
Polymers95,0012
Non-polymers1,2044
Water5,603311
1
A: Phosphoribosylamine--glycine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1033
Polymers47,5001
Non-polymers6022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphoribosylamine--glycine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1033
Polymers47,5001
Non-polymers6022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Phosphoribosylamine--glycine ligase
hetero molecules

B: Phosphoribosylamine--glycine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2056
Polymers95,0012
Non-polymers1,2044
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_544x,y-1,z-11
Buried area3630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.797, 61.623, 89.963
Angle α, β, γ (deg.)97.65, 102.98, 106.65
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Phosphoribosylamine--glycine ligase / GARS / Glycinamide ribonucleotide synthetase / Phosphoribosylglycinamide synthetase


Mass: 47500.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Plasmid: pET-21a / Production host: Escherichia coli (E. coli)
References: UniProt: O66949, phosphoribosylamine-glycine ligase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: 2.44 Å3/Da / Density % sol: 49.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1M Phosphate-citrate, 40% MPD, 10mM ATP, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 18, 2006
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: 1.8→50 Å / Num. obs: 79536 / % possible obs: 96.5 % / Redundancy: 2.8 % / Biso Wilson estimate: 14.8 Å2 / Rmerge(I) obs: 0.055
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.28 / % possible all: 95.7

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Processing

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

1gso


Resolution: 1.8→35.42 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 143384.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.227 7732 10.1 %RANDOM
Rwork0.203 ---
obs0.203 76900 92.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.3292 Å2 / ksol: 0.383349 e/Å3
Displacement parametersBiso mean: 21.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.2 Å2-0.73 Å2-1.56 Å2
2---1.3 Å2-2.29 Å2
3----0.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.8→35.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6668 0 72 311 7051
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.781.5
X-RAY DIFFRACTIONc_mcangle_it2.682
X-RAY DIFFRACTIONc_scbond_it5.932
X-RAY DIFFRACTIONc_scangle_it9.012.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.308 1107 9.7 %
Rwork0.268 10307 -
obs--82.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4atp_xplor.paramatp_xplor.top

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