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- PDB-2v9y: Human aminoimidazole ribonucleotide synthetase -

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Basic information

Entry
Database: PDB / ID: 2v9y
TitleHuman aminoimidazole ribonucleotide synthetase
ComponentsPHOSPHORIBOSYLFORMYLGLYCINAMIDINE CYCLO-LIGASE
KeywordsLIGASE / MULTIFUNCTIONAL ENZYME / STRUCTURAL GENOMICS CONSORTIUM / NUCLEOTIDE-BINDING / PURINE BIOSYNTHESIS / SGC / AIRS / GART / TRANSFERASE / ATP-BINDING / AMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE / PHOSPHORYLATION / PURINE METABOLISM / STRUCTURAL GENOMICS
Function / homology
Function and homology information


phosphoribosylamine-glycine ligase / phosphoribosylglycinamide formyltransferase 1 / adenine biosynthetic process / phosphoribosylformylglycinamidine cyclo-ligase / phosphoribosylformylglycinamidine cyclo-ligase activity / purine ribonucleoside monophosphate biosynthetic process / phosphoribosylglycinamide formyltransferase activity / phosphoribosylamine-glycine ligase activity / brainstem development / 'de novo' XMP biosynthetic process ...phosphoribosylamine-glycine ligase / phosphoribosylglycinamide formyltransferase 1 / adenine biosynthetic process / phosphoribosylformylglycinamidine cyclo-ligase / phosphoribosylformylglycinamidine cyclo-ligase activity / purine ribonucleoside monophosphate biosynthetic process / phosphoribosylglycinamide formyltransferase activity / phosphoribosylamine-glycine ligase activity / brainstem development / 'de novo' XMP biosynthetic process / Purine ribonucleoside monophosphate biosynthesis / 'de novo' AMP biosynthetic process / purine nucleotide biosynthetic process / GMP biosynthetic process / 'de novo' IMP biosynthetic process / cerebellum development / cerebral cortex development / extracellular exosome / ATP binding / metal ion binding / cytosol
Similarity search - Function
Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal 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 ...Phosphoribosyl-aminoimidazole Synthetase; Chain A, domain 2 / PurM-like C-terminal domain / PurM-like, N-terminal 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 / Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain / Phosphoribosylformylglycinamidine cyclo-ligase / Phosphoribosylglycinamide formyltransferase, active site / Phosphoribosylglycinamide formyltransferase active site. / 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 / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Rudiment single hybrid motif / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / 60s Ribosomal Protein L30; Chain: A; / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Trifunctional purine biosynthetic protein adenosine-3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWelin, M. / Lehtio, L. / Arrowsmith, C.H. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Herman, M.D. / Edwards, A.M. / Flodin, S. ...Welin, M. / Lehtio, L. / Arrowsmith, C.H. / Berglund, H. / Busam, R. / Collins, R. / Dahlgren, L.G. / Herman, M.D. / Edwards, A.M. / 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
DepositionAug 28, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 6, 2015Group: Source and taxonomy / Structure summary
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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: PHOSPHORIBOSYLFORMYLGLYCINAMIDINE CYCLO-LIGASE
B: PHOSPHORIBOSYLFORMYLGLYCINAMIDINE CYCLO-LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9485
Polymers71,6602
Non-polymers2883
Water3,063170
1
A: PHOSPHORIBOSYLFORMYLGLYCINAMIDINE CYCLO-LIGASE
hetero molecules

A: PHOSPHORIBOSYLFORMYLGLYCINAMIDINE CYCLO-LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,8524
Polymers71,6602
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area4010 Å2
ΔGint-27.4 kcal/mol
Surface area31210 Å2
MethodPQS
2
B: PHOSPHORIBOSYLFORMYLGLYCINAMIDINE CYCLO-LIGASE
hetero molecules

B: PHOSPHORIBOSYLFORMYLGLYCINAMIDINE CYCLO-LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0446
Polymers71,6602
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
Buried area3980 Å2
ΔGint-29.3 kcal/mol
Surface area29630 Å2
MethodPQS
Unit cell
Length a, b, c (Å)80.670, 80.990, 98.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.02232, 0.9998, 0.001274), (-0.9997, 0.02232, 0.002542), (0.002513, 0.00133, 1)
Vector: 39.61, 0.6257, -48.43)

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Components

#1: Protein PHOSPHORIBOSYLFORMYLGLYCINAMIDINE CYCLO-LIGASE / AMINOIMIDAZOLE RIBONUCLEOTIDE SYNTHETASE / AIRS / PHOSPHORIBOSYL-AMINOIMIDAZOLE SYNTHETASE / AIR SYNTHASE


Mass: 35830.016 Da / Num. of mol.: 2 / Fragment: RESIDUES 467-794 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): GOLD PRARE2
References: UniProt: P22102, phosphoribosylformylglycinamidine cyclo-ligase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 752 TO GLY ENGINEERED RESIDUE IN CHAIN B, ASP 752 TO GLY
Nonpolymer detailsSULFATE ION (SO4): FLEXIBLE REGION BETWEEN RESIDUE 770 AND 773 IN BOTH A AND B.
Sequence detailsSEQUENCE CONTAINED AN N-TERMINAL HEXAHISTIDINE TAG

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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: 2.29 Å3/Da / Density % sol: 46.4 % / Description: NONE
Crystal growpH: 5.2
Details: 0.1 M BIS-TRIS PH 5.2, 27% PEG 3350, 0.2 M AMMONIUM SULFATE, 0.2 MG/ML OF CHYMOTRYPSIN WAS ADDED PRIOR TO CRYSTALLISATION.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 12, 2007 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→15 Å / Num. obs: 38171 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 14.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 28.7
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 14.9 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 8.06 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0032refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CLI

1cli


Resolution: 2.1→14.99 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.916 / SU B: 9.202 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE PROTEIN WAS CO CRYSTALLIZED WITH CHYMOTRYPSIN AND THE MOST PROBABLE SEQUENCE IN THE CRYSTAL IS KVDLGGFAGLFDLKAAGFKDPLLA SGTDGVGTKL ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE PROTEIN WAS CO CRYSTALLIZED WITH CHYMOTRYPSIN AND THE MOST PROBABLE SEQUENCE IN THE CRYSTAL IS KVDLGGFAGLFDLKAAGFKDPLLA SGTDGVGTKL KIAQLCNKHD TIGQDLVAMC VNDILAQGAE PLFFLDYFSC GKLDLSVTEA VVAGIAKACG KAGCALLGGE TAEMPDMYPP GEYDLAGFAV GAMERDQKLP HLERITEGDV VVGIASSGLH SNGFSLVRKI VAKSSLQYSS PAPDGCGDQT LGDLLLTPTR IYSHSLLPVL RSGHVKAFAH ITGGGLLENI PRVLPEKLGV DLDAQTWRIP RVFSWLQQEG HLSEEEMART FNCGVGAVLV VSKEQTEQIL RGIQQHKEEA WVIGSVVARA EGSPRVKVKN LIESMQINGS VLKN
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1909 5 %RANDOM
Rwork0.191 ---
obs0.194 36261 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: 32.97 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.1→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4664 0 15 170 4849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224794
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.9786494
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1195627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.79124.688192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.6615824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5311524
X-RAY DIFFRACTIONr_chiral_restr0.10.2744
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023557
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.21950
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.23182
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2215
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.298
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7631.53171
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.25224923
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.17531817
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3514.51566
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.329 159
Rwork0.208 2593
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)
11.01770.32280.10871.71940.61822.15530.1373-0.05920.08880.0957-0.1952-0.0161-0.15240.06610.0579-0.1263-0.0093-0.006-0.11120.0323-0.114211.3732-26.16260.0021
22.3182-0.5066-1.36521.17470.30562.2641-0.1413-0.027-0.00440.04380.12310.1024-0.0069-0.110.0182-0.11370.0027-0.0251-0.15040.0176-0.112426.6465-29.240748.6642
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A475 - 792
2X-RAY DIFFRACTION2B475 - 785

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