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- PDB-3ax6: Crystal structure of N5-carboxyaminoimidazole ribonucleotide synt... -

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Basic information

Entry
Database: PDB / ID: 3ax6
TitleCrystal structure of N5-carboxyaminoimidazole ribonucleotide synthetase from Thermotoga maritima
ComponentsPhosphoribosylaminoimidazole carboxylase, ATPase subunit
KeywordsLIGASE / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / ATP grasp / ATP binding
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 / : / Ribonucleotide synthetase preATP-grasp 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 ...Phosphoribosylaminoimidazole carboxylase, ATPase subunit / Phosphoribosylaminoimidazole carboxylase, C-terminal domain / Phosphoribosylaminoimidazole carboxylase C-terminal domain / : / Ribonucleotide synthetase preATP-grasp 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
ADENOSINE-5'-DIPHOSPHATE / N5-carboxyaminoimidazole ribonucleotide synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsMiyazawa, R. / Kanagawa, M. / Baba, S. / Nakagawa, N. / Ebihara, A. / Kuramitsu, S. / Yokoyama, S. / Kawai, G. / Sampei, G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structures of N5-carboxyaminoimidazole ribonucleotide synthetase, PurK, from thermophilic bacteria
Authors: Okada, K. / Taka, H. / Tsunoda, S. / Tamura, S. / Miyazawa, R. / Baba, S. / Kanagawa, M. / Nakagawa, N. / Ebihara, A. / Kuramitsu, S. / Yokoyama, S. / Kawai, G. / Sampei, G.
History
DepositionMar 30, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Phosphoribosylaminoimidazole carboxylase, ATPase subunit
B: Phosphoribosylaminoimidazole carboxylase, ATPase subunit
C: Phosphoribosylaminoimidazole carboxylase, ATPase subunit
D: Phosphoribosylaminoimidazole carboxylase, ATPase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,2338
Polymers172,5244
Non-polymers1,7094
Water14,178787
1
A: Phosphoribosylaminoimidazole carboxylase, ATPase subunit
B: Phosphoribosylaminoimidazole carboxylase, ATPase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1164
Polymers86,2622
Non-polymers8542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-12 kcal/mol
Surface area29620 Å2
MethodPISA
2
C: Phosphoribosylaminoimidazole carboxylase, ATPase subunit
D: Phosphoribosylaminoimidazole carboxylase, ATPase subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1164
Polymers86,2622
Non-polymers8542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-10 kcal/mol
Surface area29790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.919, 186.590, 68.463
Angle α, β, γ (deg.)90.00, 90.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Phosphoribosylaminoimidazole carboxylase, ATPase subunit


Mass: 43130.938 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM_0447 / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYS8
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 787 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.37 Å3/Da / Density % sol: 48.02 % / Description: The file contains Friedel pairs.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 0.1M sodium chloride, 0.1M Bis-tris pH6.6, 25% (w/v) PEG 3350, 10mM adenosine diphosphate, 10mM magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97905,0.90000,0.97945
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 3, 2007 / Details: Toroidal Mirror
RadiationMonochromator: Fixed exit Si 111 double crystal monochromator
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979051
20.91
30.979451
ReflectionResolution: 2.2→50 Å / Num. obs: 135114 / % possible obs: 94.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 10.1 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 7.62
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 1.35 / % possible all: 83.5

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Processing

Software
NameVersionClassification
BSSdata collection
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.2→45.14 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 58306.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED. THE FILE CONTAINS FRIEDEL PAIRS.
RfactorNum. reflection% reflectionSelection details
Rfree0.268 13033 9.6 %RANDOM
Rwork0.216 ---
obs0.216 135114 84.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.0483 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 23.8 Å2
Baniso -1Baniso -2Baniso -3
1-5.38 Å20 Å21.26 Å2
2---5.68 Å20 Å2
3---0.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.2→45.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11364 0 108 787 12259
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.152
X-RAY DIFFRACTIONc_scbond_it2.272
X-RAY DIFFRACTIONc_scangle_it3.332.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 1445 8.9 %
Rwork0.315 14874 -
obs--61.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2adp.paramadp.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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