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- PDB-2z04: Crystal structure of phosphoribosylaminoimidazole carboxylase ATP... -

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Basic information

Entry
Database: PDB / ID: 2z04
TitleCrystal structure of phosphoribosylaminoimidazole carboxylase ATPase subunit from Aquifex aeolicus
ComponentsPhosphoribosylaminoimidazole carboxylase ATPase subunit
KeywordsLYASE / PURINE NUCLEOTIDE BIOSYNTHETIC PATHWAY / STRUCTURAL GENOMICS / NPPSFA / NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES / Metabolic Systems / ATP-binding / Decarboxylase / Nucleotide-binding / Purine biosynthesis / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


5-(carboxyamino)imidazole ribonucleotide synthase / 5-(carboxyamino)imidazole ribonucleotide synthase activity / phosphoribosylaminoimidazole carboxylase activity / 'de novo' IMP biosynthetic process / ATP binding / metal ion binding
Similarity search - Function
Phosphoribosylaminoimidazole carboxylase, ATPase subunit / Phosphoribosylaminoimidazole carboxylase, C-terminal domain / Phosphoribosylaminoimidazole carboxylase C-terminal domain / ATP-grasp fold, ATP-dependent carboxylate-amine ligase-type / ATP-grasp domain / Rossmann fold - #20 / Rudiment single hybrid motif / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily ...Phosphoribosylaminoimidazole carboxylase, ATPase subunit / Phosphoribosylaminoimidazole carboxylase, C-terminal domain / Phosphoribosylaminoimidazole carboxylase C-terminal domain / ATP-grasp fold, ATP-dependent carboxylate-amine ligase-type / ATP-grasp domain / Rossmann fold - #20 / Rudiment single hybrid motif / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N5-carboxyaminoimidazole ribonucleotide synthase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.35 Å
AuthorsOkada, K. / Tamura, S. / Baba, S. / Kanagawa, M. / Kawai, G. / Sampei, G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of phosphoribosylaminoimidazole carboxylase ATPase subunit from Aquifex aeolicus
Authors: Okada, K. / Tamura, S. / Baba, S. / Kanagawa, M. / Kawai, G. / Sampei, G.
History
DepositionMay 6, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoribosylaminoimidazole carboxylase ATPase subunit
B: Phosphoribosylaminoimidazole carboxylase ATPase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7714
Polymers84,5792
Non-polymers1922
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.291, 55.053, 74.541
Angle α, β, γ (deg.)93.93, 101.54, 114.23
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Phosphoribosylaminoimidazole carboxylase ATPase subunit / AIR carboxylase / AIRC


Mass: 42289.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: purK / Plasmid: pET21a / Production host: Escherichia coli (E. coli)
References: UniProt: O66608, phosphoribosylaminoimidazole carboxylase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.19 Å3/Da / Density % sol: 43.88 % / Description: The file contains Friedel pairs.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 47.5% PEG200, CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9789, 0.9793, 0.9000
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 6, 2006
RadiationMonochromator: Fixed exit double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.97931
30.91
ReflectionResolution: 2.35→32.41 Å / Num. all: 59848 / Num. obs: 56281 / % possible obs: 94 % / Observed criterion σ(F): 0 / Biso Wilson estimate: 26.7 Å2
Reflection shellResolution: 2.35→2.5 Å / Num. unique all: 8627 / % possible all: 86

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.35→32.41 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 607086.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: The file contains Friedel pairs.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 5515 9.8 %RANDOM
Rwork0.232 ---
obs0.232 50766 94 %-
all-56281 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.4616 Å2 / ksol: 0.365161 e/Å3
Displacement parametersBiso mean: 52 Å2
Baniso -1Baniso -2Baniso -3
1--3.08 Å211.93 Å2-0.11 Å2
2--14.59 Å25.83 Å2
3----11.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.35→32.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5157 0 10 40 5207
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it1.911.5
X-RAY DIFFRACTIONc_mcangle_it3.342
X-RAY DIFFRACTIONc_scbond_it2.62
X-RAY DIFFRACTIONc_scangle_it4.042.5
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.359 854 9.9 %
Rwork0.315 7773 -
obs--86 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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