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- PDB-1thz: Crystal Structure of Avian AICAR Transformylase in Complex with a... -

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Basic information

Entry
Database: PDB / ID: 1thz
TitleCrystal Structure of Avian AICAR Transformylase in Complex with a Novel Inhibitor Identified by Virtual Ligand Screening
ComponentsBifunctional purine biosynthesis protein PURH
KeywordsTRANSFERASE / HYDROLASE / ATIC / Virtual Ligand Screening / Purine biosynthesis / Cancer Target
Function / homology
Function and homology information


De novo synthesis of IMP / phosphoribosylaminoimidazolecarboxamide formyltransferase / phosphoribosylaminoimidazolecarboxamide formyltransferase activity / IMP cyclohydrolase / IMP cyclohydrolase activity / 'de novo' IMP biosynthetic process / protein homodimerization activity / cytosol
Similarity search - Function
Helix Hairpins - #440 / AICAR transformylase, insert domain superfamily / AICAR transformylase, duplication domain / AICAR transformylase, duplicated domain superfamily / AICARFT/IMPCHase bienzyme / Bifunctional purine biosynthesis protein PurH-like / AICARFT/IMPCHase bienzyme / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily ...Helix Hairpins - #440 / AICAR transformylase, insert domain superfamily / AICAR transformylase, duplication domain / AICAR transformylase, duplicated domain superfamily / AICARFT/IMPCHase bienzyme / Bifunctional purine biosynthesis protein PurH-like / AICARFT/IMPCHase bienzyme / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain profile. / MGS-like domain / Cytidine Deaminase; domain 2 / Cytidine deaminase-like / Helix Hairpins / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-326 / : / Bifunctional purine biosynthesis protein ATIC
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsXu, L. / Li, C. / Olson, A.J. / Wilson, I.A.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: Crystal structure of avian aminoimidazole-4-carboxamide ribonucleotide transformylase in complex with a novel non-folate inhibitor identified by virtual ligand screening.
Authors: Xu, L. / Li, C. / Olson, A.J. / Wilson, I.A.
#1: Journal: Biochemistry / Year: 2002
Title: Structural Insights Into the Avian Aicar Transformylase Mechanism
Authors: Wolan, D.W. / Greasley, S.E. / Bearsley, G.P. / Wilson, I.A.
#2: Journal: Biochemistry / Year: 2003
Title: Structure of Avian Aicar Transformylase with a Multisubstrate Adduct Inhibitor Beta-Dadf Identifies the Folate Binding Site
Authors: Wolan, D.W. / Greasley, S.E. / Wall, M.J. / Benkovic, S.J. / Wilson, I.A.
#3: Journal: Biochemistry / Year: 2004
Title: Structural Insights Into the Human and Avian Imp Cyclohydrolase Mechanism Via Crystal Structures with the Bound Xmp Inhibitor
Authors: Wolan, D.W. / Cheong, C.G. / Greasley, S.E. / Wilson, I.A.
#4: Journal: J.Biol.Chem. / Year: 2004
Title: Crystal structures of human bifunctional enzyme aminoimidazole-4-carboxamide ribonucleotide transformylase/IMP cyclohydrolase in complex with potent sulfonyl-containing antifolates.
Authors: Cheong, C.G. / Woland, D.W. / Greasley, S.E. / Horton, P.A. / Beardsley, G.P. / Wilson, I.A.
#5: Journal: Nat.Struct.Mol.Biol. / Year: 2001
Title: Crystal structure of a bifunctional transformylase and cyclohydrolase enzyme in purine biosynthesis.
Authors: Greasley, S.E. / Horton, P.A. / Ramcharan, J. / Bearsley, G.P. / Benkovic, S.J. / Wilson, I.A.
History
DepositionJun 1, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: Bifunctional purine biosynthesis protein PURH
B: Bifunctional purine biosynthesis protein PURH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,0676
Polymers128,9952
Non-polymers1,0714
Water13,475748
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13900 Å2
ΔGint-79 kcal/mol
Surface area44460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.800, 105.300, 102.400
Angle α, β, γ (deg.)90.00, 108.10, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiological Dimer

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Components

#1: Protein Bifunctional purine biosynthesis protein PURH


Mass: 64497.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PURH CONTAINS PHOSPHORIBOSYLAMINOIMIDAZOLECARBOXAMIDE FORMYLTRANSFERASE AND IMP CYCLOHYDROLASE
Source: (gene. exp.) Gallus gallus (chicken) / Gene: ATIC, PURH / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21.DE3
References: UniProt: P31335, phosphoribosylaminoimidazolecarboxamide formyltransferase, IMP cyclohydrolase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-326 / 2-{(E)-[5-HYDROXY-3-METHYL-1-(2-METHYL-4-SULFOPHENYL)-1H-PYRAZOL-4-YL]DIAZENYL}-4-SULFOBENZOIC ACID / 2-[5-HYDROXY-3-METHYL-1-(2-METHYL-4-SULFO-PHENYL)-1H-PYRAZOL-4-YLAZO]-4-SULFO-BENZOIC ACID


Mass: 496.471 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H16N4O9S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 748 / 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: 2.6 Å3/Da / Density % sol: 51.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: PEG8000, 0.2 M Imidazole pH 7.2, 5mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 27, 2003 / Details: mirrors
RadiationMonochromator: single crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.8→31 Å / Num. all: 120745 / Num. obs: 113750 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 21.4 Å2 / Rsym value: 0.101 / Net I/σ(I): 11.9
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 4.6 / Num. unique all: 18414 / Rsym value: 0.312 / % possible all: 92.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G8M

1g8m


Resolution: 1.8→31.01 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 825129.01 / Data cutoff low absF: 0 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood target using amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2836 2.5 %RANDOM
Rwork0.214 ---
obs0.214 113750 94.1 %-
all-120745 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.728 Å2 / ksol: 0.352455 e/Å3
Displacement parametersBiso mean: 27.3 Å2
Baniso -1Baniso -2Baniso -3
1--5.74 Å20 Å20.52 Å2
2--5.39 Å20 Å2
3---0.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.8→31.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9022 0 68 748 9838
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.95
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 457 2.5 %
Rwork0.246 17957 -
obs-18414 92.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4CIS_PEPTIDE.PARAM326203_NEW.TOP
X-RAY DIFFRACTION5326203_NEW.PAR

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