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- PDB-1oz0: CRYSTAL STRUCTURE OF THE HOMODIMERIC BIFUNCTIONAL TRANSFORMYLASE ... -

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Basic information

Entry
Database: PDB / ID: 1oz0
TitleCRYSTAL STRUCTURE OF THE HOMODIMERIC BIFUNCTIONAL TRANSFORMYLASE AND CYCLOHYDROLASE ENZYME AVIAN ATIC IN COMPLEX WITH A MULTISUBSTRATE ADDUCT INHIBITOR BETA-DADF.
ComponentsBifunctional purine biosynthesis protein PURH
KeywordsTRANSFERASE / HYDROLASE / HOMODIMER / 2 FUNCTIONAL DOMAINS / IMPCH DOMAIN = ALPHA/BETA/ALPHA / AICAR TFASE = 2 ALPHA/BETA/ALPHA DOMAINS / 1 ALPHA + BETA DOMAIN
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-MS1 / PHOSPHATE ION / Bifunctional purine biosynthesis protein ATIC
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWolan, D.W. / Greasley, S.E. / Wall, M.J. / Benkovic, S.J. / Wilson, I.A.
CitationJournal: 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.
History
DepositionApr 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,2388
Polymers133,3382
Non-polymers1,8996
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15740 Å2
ΔGint-80 kcal/mol
Surface area43240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.410, 108.100, 102.360
Angle α, β, γ (deg.)90.00, 91.92, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2
DetailsThe asymmetric unit contains the biologically active homodimer.

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Components

#1: Protein Bifunctional purine biosynthesis protein PURH / AICAR TRANSFORMYLASE-IMP CYCLOHYDROLASE / Phosphoribosylaminoimidazolecarboxamide formyltransferase ...AICAR TRANSFORMYLASE-IMP CYCLOHYDROLASE / Phosphoribosylaminoimidazolecarboxamide formyltransferase / Inosinicase / IMP synthetase / ATIC


Mass: 66669.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: ATIC OR 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MS1 / 2-[4-((2-AMINO-4-OXO-3,4-DIHYDRO-PYRIDO[3,2-D]PYRIMIDIN-6-YLMETHYL)-{3-[5-CARBAMOYL-3-(3,4- DIHYDROXY-5-PHOSPHONOOXYMETHYL-TETRAHYDRO-FURAN-2-YL)-3H-IMIDAZOL-4-YL]-ACRYLOYL}-AMINO)-BENZOYLAMINO]- PENTANEDIOIC ACID / BETA-DADF / MSA / MULTISUBSTRATE ADDUCT INHIBITOR


Mass: 815.637 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H34N9O15P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.3 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 13% (w/v) PEG 8000, 0.2M imidazole, pH 7.0 and 5mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
213 %(w/v)PEG80001reservoir
30.2 Mimidazole1reservoirpH7.0
45 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 29, 1998
Details: Flat mirror (vertical focusing); single crystal Si(311) bent monochromator (horizontal focusing)
RadiationMonochromator: NULL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 39623 / Num. obs: 39623 / % possible obs: 92.5 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 36.4 Å2 / Rsym value: 0.055 / Net I/σ(I): 14
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 1825 / Rsym value: 0.424 / % possible all: 85.8
Reflection
*PLUS
Highest resolution: 2.5 Å / Rmerge(I) obs: 0.055
Reflection shell
*PLUS
Highest resolution: 2.5 Å / % possible obs: 85.8 % / Num. unique obs: 1825 / Rmerge(I) obs: 0.424

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G8M

1g8m


Resolution: 2.5→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.269 3554 8.7 %random
Rwork0.217 ---
all-38094 --
obs-38094 92.1 %-
Displacement parametersBiso mean: 46.89 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å20 Å21.55 Å2
2--12.99 Å20 Å2
3----11.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9022 0 126 378 9526
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_torsion_deg22
X-RAY DIFFRACTIONx_torsion_impr_deg1.03
X-RAY DIFFRACTIONx_mcbond_it1.0241.5
X-RAY DIFFRACTIONx_mcangle_it1.7342
X-RAY DIFFRACTIONx_scbond_it1.3242
X-RAY DIFFRACTIONx_scangle_it2.0332.5
Refine LS restraints NCS
Ens-IDDom-IDRefine-IDRms dev position (Å)Weight Biso Weight position
11X-RAY DIFFRACTION0.07892100
22X-RAY DIFFRACTION0.90072100
LS refinement shellResolution: 2.5→2.52 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.465 60 8.6 %
Rwork0.444 --
obs-695 -
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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