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- PDB-1njs: human GAR Tfase in complex with hydrolyzed form of 10-trifluoroac... -

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Basic information

Entry
Database: PDB / ID: 1njs
Titlehuman GAR Tfase in complex with hydrolyzed form of 10-trifluoroacetyl-5,10-dideaza-acyclic-5,6,7,8-tetrahydrofolic acid
ComponentsPhosphoribosylglycinamide formyltransferase
KeywordsTRANSFERASE / protein-cofactor analogue complex
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
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 / 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 / Formyl transferase, N-terminal domain / 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. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-KEU / PHOSPHATE ION / Trifunctional purine biosynthetic protein adenosine-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsZhang, Y. / Desharnais, J. / Marsilje, T.H. / Li, C. / Hedrick, M.P. / Gooljarsingh, L.T. / Tavassoli, A. / Benkovic, S.J. / Olson, A.J. / Boger, D.L. / Wilson, I.A.
CitationJournal: Biochemistry / Year: 2003
Title: Rational Design, Synthesis, Evaluation, and Crystal Structure of a Potent Inhibitor of Human GAR Tfase: 10-(Trifluoroacetyl)-5,10-dideazaacyclic-5,6,7,8-tetrahydrofolic Acid
Authors: Zhang, Y. / Desharnais, J. / Marsilje, T.H. / Li, C. / Hedrick, M.P. / Gooljarsingh, L.T. / Tavassoli, A. / Benkovic, S.J. / Olson, A.J. / Boger, D.L. / Wilson, I.A.
History
DepositionJan 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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
Remark 600HETEROGEN The ligand has a trifluoroacetyl group when synthesized and is named 10-TRIFLUOROACETYL- ...HETEROGEN The ligand has a trifluoroacetyl group when synthesized and is named 10-TRIFLUOROACETYL-5,10-DIDEAZA-ACYCLIC-5,6,7,8- TETRAHYDROFOLIC ACID. When the compound interacts with protein human GAR Tfase, the ketone group is hydrolyzed to two hydroxyl groups ("gem-diol"). The hydrolyzed form was the binding form in the structure. The hydrolyzed compound is only stable when bound to enzyme.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoribosylglycinamide formyltransferase
B: Phosphoribosylglycinamide formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7427
Polymers45,3582
Non-polymers1,3845
Water4,522251
1
A: Phosphoribosylglycinamide formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4184
Polymers22,6791
Non-polymers7393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphoribosylglycinamide formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3233
Polymers22,6791
Non-polymers6442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.235, 126.235, 94.419
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Phosphoribosylglycinamide formyltransferase / GAR TFASE / GART / GAR transformylase / 5'-phosphoribosylglycinamide transformylase


Mass: 22678.941 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GART / Production host: Escherichia coli (E. coli)
References: UniProt: P22102, phosphoribosylglycinamide formyltransferase 1
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-KEU / N-{4-[(1R)-4-[(2R,4R,5S)-2,4-DIAMINO-6-OXOHEXAHYDROPYRIMIDIN-5-YL]-1-(2,2,2-TRIFLUORO-1,1-DIHYDROXYETHYL)BUTYL]BENZOYL}-D-GLUTAMIC ACID / 10-CF3C(OH)2-DDACTHF / HYDROLYZED FORM OF 10-TRIFLUOROACETYL-5,10-DIDEAZA-ACYCLIC-5,6,7,8-TETRAHYDROFOLIC ACID


Mass: 549.498 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H30F3N5O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 4.79 Å3/Da / Density % sol: 74.3 %
Crystal growTemperature: 282 K / Method: vapor diffusion, sitting drop
Details: PEG4K, 0.2 Ammonium Sulfate, 50mM HEPES 6.7-7.0, VAPOR DIFFUSION, SITTING DROP, temperature 282K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop / PH range low: 7 / PH range high: 6.7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
20.2 Mammonium sulfate1reservoir
350 mMHEPES1reservoirpH6.7-7.0
416 mg/mlprotein1drop
1PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2002
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 1.98→41.32 Å / Num. all: 60661 / Num. obs: 57912 / % possible obs: 95.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.88 % / Rsym value: 0.074 / Net I/σ(I): 25
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 3.91 % / Mean I/σ(I) obs: 2.02 / Num. unique all: 2996 / Rsym value: 0.601 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 45 Å / % possible obs: 99.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
% possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.601 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
REFMAC5.1.24refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1MEJ

1mej


Resolution: 1.98→41.32 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.907 / SU B: 2.765 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.125 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24732 2913 5 %RANDOM
Rwork0.2269 ---
obs0.22794 54999 96 %-
all-57912 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.295 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.09 Å20 Å2
2---0.17 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.98→41.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3014 0 91 251 3356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213152
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3691.9864286
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9785398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1350.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022294
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.21435
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2254
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.232
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0680.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6141.51992
X-RAY DIFFRACTIONr_mcangle_it1.14823216
X-RAY DIFFRACTIONr_scbond_it2.14631160
X-RAY DIFFRACTIONr_scangle_it3.5654.51070
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.981→2.033 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.291 196
Rwork0.246 3599
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)
11.6259-0.98030.10611.74760.14211.2617-0.00760.03990.0267-0.14130.0124-0.280.07160.1541-0.00480.0441-0.01570.02010.01330.00950.045273.641917.983522.9917
22.8273-1.1998-0.25461.43250.10931.1178-0.0602-0.28440.21960.14140.09310.0313-0.2453-0.1538-0.03290.10030.0348-0.01440.07530.00460.036643.360741.771224.6335
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2001 - 200
2X-RAY DIFFRACTION2BB1 - 2001 - 200
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.247 / Rfactor Rwork: 0.227
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.37

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