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- PDB-2ywx: Crystal structure of phosphoribosylaminoimidazole carboxylase cat... -

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Basic information

Entry
Database: PDB / ID: 2ywx
TitleCrystal structure of phosphoribosylaminoimidazole carboxylase catalytic subunit from Methanocaldococcus jannaschii
ComponentsPhosphoribosylaminoimidazole carboxylase catalytic subunit
KeywordsLYASE / Rossmann fold / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


5-(carboxyamino)imidazole ribonucleotide mutase / 5-(carboxyamino)imidazole ribonucleotide mutase activity / 'de novo' IMP biosynthetic process
Similarity search - Function
: / Class I PurE / PurE, prokaryotic type / PurE domain / AIR carboxylase / AIR carboxylase / Rossmann fold - #1970 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N5-carboxyaminoimidazole ribonucleotide mutase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsKanagawa, M. / Baba, S. / Kuramitsu, S. / Yokoyama, S. / Kawai, G. / Sampei, G. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of phosphoribosylaminoimidazole carboxylase catalytic subunit from Methanocaldococcus jannaschii
Authors: Kanagawa, M. / Baba, S. / Kuramitsu, S. / Yokoyama, S. / Kawai, G. / Sampei, G.
History
DepositionApr 23, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoribosylaminoimidazole carboxylase catalytic subunit


Theoretical massNumber of molelcules
Total (without water)16,9741
Polymers16,9741
Non-polymers00
Water45025
1
A: Phosphoribosylaminoimidazole carboxylase catalytic subunit
x 8


Theoretical massNumber of molelcules
Total (without water)135,7928
Polymers135,7928
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area32880 Å2
ΔGint-201 kcal/mol
Surface area41610 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)100.887, 100.887, 70.912
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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


Mass: 16974.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Plasmid: pET-21a / Production host: Escherichia coli (E. coli)
References: UniProt: Q58033, phosphoribosylaminoimidazole carboxylase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.66 Å3/Da / Density % sol: 53.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.4
Details: 0.1M Natrium Acetate(pH 4.4), 3.2M Natrium Chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 18, 2007
RadiationMonochromator: Fixed exit Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.31→50 Å / Num. obs: 8318 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 31.9 Å2 / Rmerge(I) obs: 0.075
Reflection shellResolution: 2.31→2.39 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.415 / Num. unique all: 1545 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O4V

1o4v


Resolution: 2.31→31.9 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 509961.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24 855 10.6 %RANDOM
Rwork0.23 ---
obs0.23 8105 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.2955 Å2 / ksol: 0.351168 e/Å3
Displacement parametersBiso mean: 46.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.11 Å20 Å20 Å2
2---3.11 Å20 Å2
3---6.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.31→31.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1188 0 0 25 1213
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.31→2.45 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.265 117 9.2 %
Rwork0.287 1157 -
obs--93.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4xmp_xplor.parmxmp_xplor.top

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