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- PDB-1gso: GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE (GAR-SYN) FROM E. COLI. -

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Basic information

Entry
Database: PDB / ID: 1gso
TitleGLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE (GAR-SYN) FROM E. COLI.
ComponentsPROTEIN (GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE)
KeywordsLIGASE / GAR-SYN / GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE / ATP-GRASP / PURINE DE NOVO BIOSYNTHETIC PATHWAY / SUBSTRATE CHANNELING
Function / homology
Function and homology information


purine nucleobase biosynthetic process / phosphoribosylamine-glycine ligase / phosphoribosylamine-glycine ligase activity / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / DNA damage response / ATP hydrolysis activity / 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, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold, B domain / 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
Phosphoribosylamine--glycine ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsWang, W. / Kappock, T.J. / Stubbe, J. / Ealick, S.E.
Citation
Journal: Biochemistry / Year: 1998
Title: X-ray crystal structure of glycinamide ribonucleotide synthetase from Escherichia coli.
Authors: Wang, W. / Kappock, T.J. / Stubbe, J. / Ealick, S.E.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Purification, Crystallization and Preliminary X-Ray Diffraction Data from Selenomethione Glycinamide Ribonucleotide Synthetase
Authors: Weaver, T.M. / Wang, W. / Ealick, S.E.
History
DepositionSep 8, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 9, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE)


Theoretical massNumber of molelcules
Total (without water)46,2841
Polymers46,2841
Non-polymers00
Water5,386299
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.220, 62.420, 129.770
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 PROTEIN (GLYCINAMIDE RIBONUCLEOTIDE SYNTHETASE) / PURD GEN PRODUCT


Mass: 46283.527 Da / Num. of mol.: 1 / Mutation: P294L / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Cell line: B834(DE3) / Strain: TX635
References: UniProt: P15640, phosphoribosylamine-glycine ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.47 Å3/Da / Density % sol: 50 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.3
Details: 0.1M MES PH6.3, 0.2M AMMONIUM SULFATE, 26% PEG 5K MONOMETHYLETHER, HANGING DROP VAPOR DEFFUSION, vapor diffusion - hanging drop
Crystal
*PLUS
Density % sol: 50 %
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MMES1reservoir
20.1 Mammonium sulfate1reservoir
324 %PEG MME50001reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.979419, 0.979104, 0.967642, 0.9190
DetectorType: ADSC / Detector: CCD / Date: Aug 1, 1997
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9794191
20.9791041
30.9676421
40.9191
ReflectionResolution: 1.6→20 Å / Num. obs: 58385 / % possible obs: 95.9 % / Redundancy: 5.2 % / Rsym value: 4.3 / Net I/σ(I): 10
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 4.1 / Rsym value: 17.4 / % possible all: 83.9
Reflection
*PLUS
Rmerge(I) obs: 0.043
Reflection shell
*PLUS
% possible obs: 83.9 % / Num. unique obs: 7256 / Rmerge(I) obs: 0.174

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Processing

Software
NameVersionClassification
MADSYSphasing
SnBphasing
MLPHAREphasing
DMmodel building
X-PLOR3.851refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 1.6→10 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.247 5925 10 %RANDOM
Rwork0.209 ---
obs0.209 58307 95 %-
Displacement parametersBiso mean: 22.1 Å2
Refine analyzeLuzzati coordinate error free: 0.24 Å
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3161 0 0 305 3466
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.25
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.15
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.6→1.67 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.307 604 10 %
Rwork0.298 5578 -
obs--81.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 10 Å / σ(F): 3 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.15
LS refinement shell
*PLUS
Highest resolution: 1.6 Å / Rfactor Rfree: 0.307 / % reflection Rfree: 10 % / Rfactor Rwork: 0.298

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