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- PDB-1g8m: CRYSTAL STRUCTURE OF AVIAN ATIC, A BIFUNCTIONAL TRANSFORMYLASE AN... -

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Basic information

Entry
Database: PDB / ID: 1g8m
TitleCRYSTAL STRUCTURE OF AVIAN ATIC, A BIFUNCTIONAL TRANSFORMYLASE AND CYCLOHYDROLASE ENZYME IN PURINE BIOSYNTHESIS AT 1.75 ANG. RESOLUTION
ComponentsAICAR TRANSFORMYLASE-IMP CYCLOHYDROLASE
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 / 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
GUANOSINE-5'-MONOPHOSPHATE / : / Bifunctional purine biosynthesis protein ATIC
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsGreasley, S.E. / Horton, P. / Beardsley, G.P. / Benkovic, S.J. / Wilson, I.A.
CitationJournal: 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.
History
DepositionNov 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AICAR TRANSFORMYLASE-IMP CYCLOHYDROLASE
B: AICAR TRANSFORMYLASE-IMP CYCLOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,3755
Polymers129,9332
Non-polymers4413
Water13,403744
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12780 Å2
ΔGint-65 kcal/mol
Surface area43880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.100, 106.000, 103.500
Angle α, β, γ (deg.)90.00, 108.00, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein AICAR TRANSFORMYLASE-IMP CYCLOHYDROLASE / E.C.2.1.2.3, E.C.3.5.4.10 / BIFUNCTIONAL PURINE BIOSYNTHESIS PROTEIN PURH [INCLUDES PHOSPHORIBOSYLAMINOIMIDAZOLECARBOXAMIDE ...BIFUNCTIONAL PURINE BIOSYNTHESIS PROTEIN PURH [INCLUDES PHOSPHORIBOSYLAMINOIMIDAZOLECARBOXAMIDE FORMYLTRANSFERASE (AICAR TRANSFORMYLASE) AND IMP CYCLOHYDROLASE (INOSINICASE / IMP SYNTHETASE / ATIC)]


Mass: 64966.656 Da / Num. of mol.: 2
Fragment: AMINOIMIDAZOLE CARBOXAMIDE RIBONUCLEOTIDE TRANSFORMYLASE - INOSINE MONOPHOSPHATE CYCLOHYDROLASE
Mutation: MET REPLACED BY SE-MET (MSE)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: PURH / Plasmid: PET 28A / Production host: Escherichia coli (E. coli) / Strain (production host): B834(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-G / GUANOSINE-5'-MONOPHOSPHATE / Guanosine monophosphate


Type: RNA linking / Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 744 / 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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: PEG 8000, imidazole-HCl and DTT, pH 7.2, VAPOR DIFFUSION, SITTING DROP at 295K
Crystal
*PLUS
Density % sol: 53 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlenzyme1drop
225 mMTris-HCl1drop
3150 mM1dropNaCl
450 mM1dropKCl
55 mMdithiothreitol1drop
65 mMEDTA1drop
715 %(w/v)PEG80001reservoir
80.2 Mimidazole1reservoir
95 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9799 / Wavelength: 0.9799, 0.9801, 0.9648
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 3, 1999
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97991
20.98011
30.96481
ReflectionResolution: 1.75→50 Å / Num. all: 229603 / Num. obs: 229603 / % possible obs: 87.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 15.8
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 2 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 2.4 / % possible all: 47.3
Reflection
*PLUS
Num. measured all: 460370
Reflection shell
*PLUS
% possible obs: 47.3 %

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Processing

Software
NameVersionClassification
SOLVEphasing
SHARPphasing
ARP/wARPmodel building
CNS0.9refinement
Adxvdata processing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.75→50 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1962794.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2164 11992 10 %RANDOM
Rwork0.1996 ---
obs-119759 89.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.74 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso mean: 19.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å2-0.09 Å2
2--2.97 Å20 Å2
3----2.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9025 0 26 744 9795
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it0.791.5
X-RAY DIFFRACTIONc_mcangle_it1.32
X-RAY DIFFRACTIONc_scbond_it1.412
X-RAY DIFFRACTIONc_scangle_it2.122.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.288 1172 10.2 %
Rwork0.256 10362 -
obs-11534 51.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4GMP.PARGMP.TOP
X-RAY DIFFRACTION5CIS_PEPTIDE.PARAM
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81

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