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Basic information

Entry
Database: PDB / ID: 2b1g
TitleCrystal structures of transition state analogue inhibitors of inosine monophosphate cyclohydrolase
ComponentsBifunctional purine biosynthesis protein PURH
KeywordsTRANSFERASE / HYDROLASE / ATIC / IMPCH / structure-base / transition state analogue / inhibitor
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-13A / : / PHOSPHATE ION / Bifunctional purine biosynthesis protein ATIC
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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. / Wolan, D.W. / Wilson, I.A. / Olson, A.J.
#3: 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. / 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
DepositionSep 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)258,97812
Polymers257,9914
Non-polymers9878
Water7,674426
1
A: Bifunctional purine biosynthesis protein PURH
B: Bifunctional purine biosynthesis protein PURH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,4896
Polymers128,9952
Non-polymers4934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13080 Å2
ΔGint-63 kcal/mol
Surface area43370 Å2
MethodPISA, PQS
2
C: Bifunctional purine biosynthesis protein PURH
D: Bifunctional purine biosynthesis protein PURH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,4896
Polymers128,9952
Non-polymers4934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12860 Å2
ΔGint-67 kcal/mol
Surface area43500 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)57.200, 62.000, 196.600
Angle α, β, γ (deg.)80.80, 81.50, 90.00
Int Tables number1
Space group name H-MP1
DetailsThe biological unit is a dimer. There are 2 biological units in the asymmetric unit (chains A, B, C &D)

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Components

#1: Protein
Bifunctional purine biosynthesis protein PURH


Mass: 64497.703 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Includes Phosphoribosylaminoimidazolecarboxamide formyltransferase (AICAR transformylase), IMP cyclohydrolase (Inosinicase, IMP synthetase, ATIC)
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, IMP cyclohydrolase, phosphoribosylaminoimidazolecarboxamide formyltransferase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-13A / 7-(3,4-DIHYDROXY-5R-HYDROXYMETHYLTETRAHYDROFURAN-2-YL)-2,2-DIOXO-1,2R,3R,7-TETRAHYDRO-2L6-IMIDAZO[4,5-C][1,2,6]THIADIAZIN-4S-ONE


Mass: 320.279 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12N4O7S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / 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: 52.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: PEG 8000, imidazole, DTT, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1271 Å
DetectorType: ADSC / Detector: CCD / Date: Apr 7, 2004
RadiationMonochromator: double crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionNumber: 131382 / Rmerge(I) obs: 0.06 / Χ2: 1.361 / D res high: 2.1 Å / D res low: 50 Å / % possible obs: 83.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
2.12.1442.210.3510.59
5.75089.610.0461.364
4.525.793.410.051.528
3.954.5294.210.0511.572
3.593.9595.210.0541.668
3.333.5995.910.061.717
3.143.3396.110.071.678
2.983.1496.810.0831.607
2.852.9896.810.0941.598
2.742.859710.1031.405
2.652.7496.410.1181.251
2.562.6594.510.1311.161
2.492.5688.410.1481.043
2.422.4984.810.1610.935
2.372.4281.310.1710.945
2.312.377710.1940.873
2.262.3173.710.2210.782
2.222.2669.310.2540.714
2.182.2260.810.2840.666
2.142.184810.2940.609
ReflectionResolution: 2.1→50 Å / Num. all: 131382 / Num. obs: 118497 / % possible obs: 83.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Biso Wilson estimate: 38.2 Å2 / Rsym value: 0.06 / Χ2: 1.361 / Net I/σ(I): 11.4
Reflection shellResolution: 2.1→2.14 Å / % possible obs: 42.2 % / Redundancy: 1.2 % / Mean I/σ(I) obs: 1.3 / Num. measured obs: 3334 / Num. unique all: 3334 / Rsym value: 0.351 / Χ2: 0.59 / % possible all: 42.2

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Phasing

Phasing MRRfactor: 46.9 / Cor.coef. Fo:Fc: 36.8
Highest resolutionLowest resolution
Rotation4 Å20 Å
Translation4 Å15 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT1.7data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1G8M

1g8m


Resolution: 2.1→41.89 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.925 / SU B: 12.13 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.288 / ESU R Free: 0.215 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2967 2.5 %RANDOM
Rwork0.199 ---
all0.2 131382 --
obs0.243 118496 93.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.044 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å2-0.16 Å20.04 Å2
2---0.71 Å20.25 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.1→41.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18044 0 56 426 18526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02218434
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.96625012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.60152356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.05324.041772
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.83153148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.31115124
X-RAY DIFFRACTIONr_chiral_restr0.0870.22881
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213802
X-RAY DIFFRACTIONr_nbd_refined0.2120.28511
X-RAY DIFFRACTIONr_nbtor_refined0.30.212711
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2809
X-RAY DIFFRACTIONr_metal_ion_refined0.1330.212
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1720.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.211
X-RAY DIFFRACTIONr_mcbond_it0.5161.511756
X-RAY DIFFRACTIONr_mcangle_it0.963218916
X-RAY DIFFRACTIONr_scbond_it1.67136740
X-RAY DIFFRACTIONr_scangle_it2.6474.56096
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 108 -
Rwork0.258 4196 -
all-4304 -
obs-2209 84.36 %

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