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- PDB-2qk4: Human glycinamide ribonucleotide synthetase -

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Basic information

Entry
Database: PDB / ID: 2qk4
TitleHuman glycinamide ribonucleotide synthetase
ComponentsTrifunctional purine biosynthetic protein adenosine-3
KeywordsLIGASE / PURINE SYNTHESIS / ENZYME / PROTEIN-ATP COMPLEX / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


phosphoribosylformylglycinamidine cyclo-ligase / phosphoribosylformylglycinamidine cyclo-ligase activity / adenine biosynthetic process / phosphoribosylamine-glycine ligase / phosphoribosylamine-glycine ligase activity / phosphoribosylglycinamide formyltransferase 1 / purine ribonucleoside monophosphate biosynthetic process / phosphoribosylglycinamide formyltransferase activity / 'de novo' XMP biosynthetic process / brainstem development ...phosphoribosylformylglycinamidine cyclo-ligase / phosphoribosylformylglycinamidine cyclo-ligase activity / adenine biosynthetic process / phosphoribosylamine-glycine ligase / phosphoribosylamine-glycine ligase activity / phosphoribosylglycinamide formyltransferase 1 / purine ribonucleoside monophosphate biosynthetic process / phosphoribosylglycinamide formyltransferase activity / 'de novo' XMP biosynthetic process / brainstem development / Purine ribonucleoside monophosphate biosynthesis / glycine metabolic process / 'de novo' AMP biosynthetic process / GMP biosynthetic process / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / : / tetrahydrofolate biosynthetic process / cerebellum development / : / cerebral cortex development / extracellular exosome / ATP binding / metal ion binding / cytosol
Similarity search - Function
Phosphoribosylglycinamide synthetase, C-terminal domain / Glycinamide Ribonucleotide Synthetase; Chain A, domain 4 / Phosphoribosylformylglycinamidine cyclo-ligase / Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain / 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, C-terminal domain / Glycinamide Ribonucleotide Synthetase; Chain A, domain 4 / Phosphoribosylformylglycinamidine cyclo-ligase / Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain / 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 formyltransferase / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / Phosphoribosylglycinamide formyltransferase, active site / Phosphoribosylglycinamide formyltransferase active site. / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / 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 / Trifunctional purine biosynthetic protein adenosine-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsLehtio, L. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Herman, M.D. / Edwards, A. / Flodin, S. ...Lehtio, L. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Herman, M.D. / Edwards, A. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg-Schiavone, L. / Johansson, I. / Kallas, A. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nyman, T. / Persson, C. / Sagemark, J. / Stenmark, P. / Sundstrom, M. / Thorsell, A.G. / Tresaugues, L. / van den Berg, S. / Weigelt, J. / Nordlund, P. / Structural Genomics Consortium (SGC)
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: Structural studies of tri-functional human GART.
Authors: Welin, M. / Grossmann, J.G. / Flodin, S. / Nyman, T. / Stenmark, P. / Tresaugues, L. / Kotenyova, T. / Johansson, I. / Nordlund, P. / Lehtio, L.
History
DepositionJul 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 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_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_ref_seq_dif.details / _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: Trifunctional purine biosynthetic protein adenosine-3
B: Trifunctional purine biosynthetic protein adenosine-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,19812
Polymers96,5532
Non-polymers1,64610
Water2,000111
1
A: Trifunctional purine biosynthetic protein adenosine-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0996
Polymers48,2761
Non-polymers8235
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Trifunctional purine biosynthetic protein adenosine-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0996
Polymers48,2761
Non-polymers8235
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.280, 79.810, 113.870
Angle α, β, γ (deg.)90.00, 104.07, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAsymmetric unit contains two biological monomers of this domain.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Trifunctional purine biosynthetic protein adenosine-3 / [Includes: Phosphoribosylamine-glycine ligase (EC 6.3.4.13) (GARS) (Glycinamide ribonucleotide ...[Includes: Phosphoribosylamine-glycine ligase (EC 6.3.4.13) (GARS) (Glycinamide ribonucleotide synthetase) (Phosphoribosylglycinamide synthetase) / Phosphoribosylformylglycinamidine cyclo-ligase (EC 6.3.3.1) (AIRS) (Phosphoribosyl-aminoimidazole synthetase) (AIR synthase) / Phosphoribosylglycinamide formyltransferase (EC 2.1.2.2) (GART) (GAR transformylase) (5'-phosphoribosylglycinamide transformylase)]


Mass: 48276.340 Da / Num. of mol.: 2 / Fragment: N-terminal domain: residues 1-430
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GART, PGFT, PRGS / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold pRARE2
References: UniProt: P22102, phosphoribosylamine-glycine ligase

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Non-polymers , 5 types, 121 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 3.21 Å3/Da / Density % sol: 61.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 16% PEG 3350, 0.3M LiSO4, 100 mM Bis-Tris pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 25, 2007 / Details: mirrors
RadiationMonochromator: Diamond (111), Ge (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.45→20 Å / Num. all: 44786 / Num. obs: 44786 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 55.7 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 22.15
Reflection shellResolution: 2.45→2.5 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 3.94 / Num. unique all: 2434 / % possible all: 91.7

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Processing

Software
NameVersionClassification
REFMAC5.3.0032refinement
ProDCdata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GSO

1gso


Resolution: 2.45→19.98 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / SU B: 10.919 / SU ML: 0.146 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.266 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22107 2240 5 %RANDOM
Rwork0.17137 ---
obs0.17386 42544 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.959 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.45→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6262 0 98 111 6471
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226466
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.998766
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2155838
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67225.021237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.967151076
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5071524
X-RAY DIFFRACTIONr_chiral_restr0.0980.21014
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024734
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2140.22749
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3220.54455
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.3452
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2640.39
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.82424252
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.05636668
X-RAY DIFFRACTIONr_scbond_it5.38652440
X-RAY DIFFRACTIONr_scangle_it7.46362098
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 152 -
Rwork0.247 2883 -
obs--100 %
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)
11.6581-0.1337-0.54620.79570.17823.101-0.0524-0.2217-0.36060.36540.0031-0.06720.48830.43770.04930.1022-0.01580.0123-0.0601-0.0051-0.1415-8.9745-0.422887.5117
20.0446-0.1942-0.05761.6468-1.12072.4191-0.1247-0.3506-0.20180.65530.28590.29330.2940.0663-0.16120.4499-0.04960.12770.0950.0827-0.0476-21.371.7951104.8961
32.667-0.7759-0.32811.9467-0.11352.6424-0.0201-0.33760.10910.50560.1014-0.1684-0.21860.3382-0.08130.1276-0.12910.0374-0.1352-0.0602-0.207-13.775316.55294.0307
42.9786-0.0272-0.85381.62690.47352.16490.03020.0788-0.3601-0.105-0.00320.15360.4305-0.0491-0.02710.09110.0171-0.0372-0.1326-0.0609-0.1211-20.5944-10.3748.6105
50.94090.4532-0.84091.7342-0.03590.98420.03750.0099-0.1267-0.01190.01080.78940.3765-0.5216-0.04830.0905-0.092-0.0828-0.0119-0.01140.2435-40.9109-7.826654.175
62.899-0.6361-0.32662.18020.38142.82340.24640.10930.3916-0.2801-0.12040.2266-0.2006-0.1391-0.1261-0.03550.037-0.0059-0.27-0.0296-0.0826-27.69067.219150.8535
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA34 - 13156 - 153
2X-RAY DIFFRACTION2AA132 - 234154 - 256
3X-RAY DIFFRACTION3AA235 - 429257 - 451
4X-RAY DIFFRACTION4BB36 - 13158 - 153
5X-RAY DIFFRACTION5BB132 - 234154 - 256
6X-RAY DIFFRACTION6BB235 - 430257 - 452

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