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Basic information

Entry
Database: PDB / ID: 2iu3
TitleCrystal structures of transition state analogue inhibitors of inosine monophosphate cyclohydrolase
ComponentsBIFUNCTIONAL PURINE BIOSYNTHESIS PROTEIN PURH
KeywordsHYDROLASE / MULTIFUNCTIONAL ENZYME / TRANSITION STATE ANALOGUE / ATIC / IMPCH / INHIBITOR / TRANSFERASE / STRUCTURE-BASE / PURINE BIOSYNTHESIS
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 / MGS-like domain profile. / Methylglyoxal synthase-like domain ...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 / MGS-like domain profile. / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / 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-203 / : / Bifunctional purine biosynthesis protein ATIC
Similarity search - Component
Biological speciesGALLUS GALLUS (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsXu, L. / Chong, Y. / Hwang, I. / D'Onofrio, A. / Amore, K. / Beardsley, G.P. / Li, C. / Olson, A.J. / Boger, D.L. / Wilson, I.A.
Citation
Journal: J. Biol. Chem. / Year: 2007
Title: Structure-based design, synthesis, evaluation, and crystal structures of transition state analogue inhibitors of inosine monophosphate cyclohydrolase.
Authors: Xu, L. / Chong, Y. / Hwang, I. / D'Onofrio, A. / Amore, K. / Beardsley, G.P. / Li, C. / Olson, A.J. / Boger, D.L. / Wilson, I.A.
#1: Journal: J.Biol.Chem. / Year: 2004
Title: Crystal Structure of Avian Aicar 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.
#2: Journal: J.Med.Chem. / Year: 2004
Title: Successful Virtual Screening for Human Aicar Transformylase Inhibitors Against Nci Diversity Set Using Autodock
Authors: Li, C. / Xu, L. / Olson, A.J. / Wilson, I.A.
#3: Journal: Nat.Struct.Biol. / Year: 2001
Title: Crystal Structure of a Bifunctional Transformylase and Cyclohydrolase Enzyme in Purine Biosynthesis
Authors: Greasley, S.E. / Horton, P. / Ramcharan, J. / Beardsley, G.P. / Benkovic, S.J. / Wilson, I.A.
#4: Journal: Biochemistry / Year: 2002
Title: Structural Insights Into the Avian Aicar Transformylase Mechanism
Authors: Wolan, D.W. / Greasley, S.E. / Beardsley, G.P. / Wilson, I.A.
#5: 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.
#6: 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.
#7: 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. / Wolan, D.W. / Greasley, S.E. / Horton, P.A. / Beardsley, G.P. / Wilson, I.A.
History
DepositionMay 27, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Structure summary
Category: citation / entity_src_gen / struct
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _struct.title
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.5Dec 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 / pdbx_struct_conn_angle / struct_conn
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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)129,2625
Polymers128,9952
Non-polymers2663
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)387.000, 57.000, 62.100
Angle α, β, γ (deg.)90.00, 98.90, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.8023, -0.1781, 0.5697), (-0.1882, -0.9812, 0.0416), (-0.5664, 0.0739, -0.8208)
Vector: 39.1, 25.1, 116)

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Components

#1: Protein BIFUNCTIONAL PURINE BIOSYNTHESIS PROTEIN PURH / AMINOIMIDAZOLE CARBOXAMIDE RIBONUCLEOTIDE TRANSFORMYLASE AND IMP CYCLOHYDROLASE / ATIC / ...AMINOIMIDAZOLE CARBOXAMIDE RIBONUCLEOTIDE TRANSFORMYLASE AND IMP CYCLOHYDROLASE / ATIC / INOSINICASE / IMP AICAR TRANSFORMYLASE CYCLOHYDROLASE / IMP SYNTHETASE


Mass: 64497.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: BIFUNCTIONAL ENZYME / Source: (gene. exp.) GALLUS GALLUS (chicken) / Plasmid: PET28A / Production host: Escherichia coli BL21(DE3) (bacteria)
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-203 / 1,5-DIHYDROIMIDAZO[4,5-C][1,2,6]THIADIAZIN-4(3H)-ONE 2,2-DIOXIDE


Mass: 188.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N4O3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 52 %
Crystal growpH: 7.2
Details: 20%PEG8000, 0.2 M IMIDAZOLE PH7.2, 5MM DTT, 0.01M HEXAMINECOBALT TRICHLORIDE, pH 7.20

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 14, 2006 / Details: MIRROR
RadiationMonochromator: SIDE SCATTERING BENT CUBE- ROOT-BEAM SINGLE CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 30321 / % possible obs: 98 % / Observed criterion σ(I): 4 / Redundancy: 3.1 % / Biso Wilson estimate: 34.1 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.1
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.5 / % possible all: 93

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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: 2.9→35.2 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 91596.98 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.1 / Stereochemistry target values: MAXIUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.3 1102 4 %RANDOM
Rwork0.215 ---
obs0.215 27778 91.5 %-
Solvent computationSolvent model: BULK SOLVENT CORRECTION / Bsol: 22.34 Å2 / ksol: 0.279 e/Å3
Displacement parametersBiso mean: 45.8 Å2
Baniso -1Baniso -2Baniso -3
1--10.27 Å20 Å21.65 Å2
2--6.73 Å20 Å2
3---3.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 2.9→35.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9022 0 14 97 9133
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.029
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d7.25
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAIN
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.384 143 3.6 %
Rwork0.338 3780 -
obs--78.6 %
Xplor fileSerial no: 1 / Param file: YC103.PAR / Topol file: YC103.TOP

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