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- PDB-2fw8: Structure of PurE (N5-carboxyaminoimidazole ribonucleotide mutase... -

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Basic information

Entry
Database: PDB / ID: 2fw8
TitleStructure of PurE (N5-carboxyaminoimidazole ribonucleotide mutase) H89G from the acidophilic bacterium Acetobacter aceti, at pH 8
ComponentsN5-carboxyaminoimidazole ribonucleotide mutase
KeywordsLYASE / acidophile / PurE / purine biosynthesis
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 speciesAcetobacter aceti (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.75 Å
AuthorsStarks, C.M. / Kappock, T.J.
CitationJournal: Biochemistry / Year: 2006
Title: Biochemical and Structural Studies of N(5)-Carboxyaminoimidazole Ribonucleotide Mutase from the Acidophilic Bacterium Acetobacter aceti.
Authors: Constantine, C.Z. / Starks, C.M. / Mill, C.P. / Ransome, A.E. / Karpowicz, S.J. / Francois, J.A. / Goodman, R.A. / Kappock, T.J.
History
DepositionFeb 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N5-carboxyaminoimidazole ribonucleotide mutase
B: N5-carboxyaminoimidazole ribonucleotide mutase


Theoretical massNumber of molelcules
Total (without water)37,6032
Polymers37,6032
Non-polymers00
Water6,810378
1
A: N5-carboxyaminoimidazole ribonucleotide mutase
B: N5-carboxyaminoimidazole ribonucleotide mutase

A: N5-carboxyaminoimidazole ribonucleotide mutase
B: N5-carboxyaminoimidazole ribonucleotide mutase

A: N5-carboxyaminoimidazole ribonucleotide mutase
B: N5-carboxyaminoimidazole ribonucleotide mutase

A: N5-carboxyaminoimidazole ribonucleotide mutase
B: N5-carboxyaminoimidazole ribonucleotide mutase


Theoretical massNumber of molelcules
Total (without water)150,4138
Polymers150,4138
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area31050 Å2
ΔGint-150 kcal/mol
Surface area37540 Å2
MethodPISA, PQS
2
A: N5-carboxyaminoimidazole ribonucleotide mutase
B: N5-carboxyaminoimidazole ribonucleotide mutase
x 8


Theoretical massNumber of molelcules
Total (without water)300,82616
Polymers300,82616
Non-polymers00
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_653-x+1,y,-z-21
crystal symmetry operation6_563x,-y+1,-z-21
crystal symmetry operation7_553y,x,-z-21
crystal symmetry operation8_663-y+1,-x+1,-z-21
Buried area66210 Å2
ΔGint-329 kcal/mol
Surface area70970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.603, 99.603, 164.417
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 N5-carboxyaminoimidazole ribonucleotide mutase


Mass: 18801.615 Da / Num. of mol.: 2 / Mutation: H89G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetobacter aceti (bacteria) / Strain: 1023 / Gene: purE / Plasmid: pET-23a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus / References: UniProt: Q2QJL3
#2: 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: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2 M lithium sulfate 0.1 M Tris pH 8 30% (w/v) PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 111 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 15, 2005
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 40066 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Redundancy: 7.9 % / Biso Wilson estimate: 20.8 Å2 / Rsym value: 0.042 / Net I/σ(I): 36.3
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 5.4 / Num. unique all: 3269 / Rsym value: 0.29 / % possible all: 78.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1U11

1u11


Resolution: 1.75→35.22 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 764863.09 / 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
Rfree0.197 1982 5 %RANDOM
Rwork0.174 ---
obs0.174 39519 94.1 %-
all-40066 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.7802 Å2 / ksol: 0.361804 e/Å3
Displacement parametersBiso mean: 20.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å20 Å2
2---0.83 Å20 Å2
3---1.66 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.75→35.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2298 0 0 378 2676
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.031.5
X-RAY DIFFRACTIONc_mcangle_it1.582
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it2.722.5
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.294 283 5 %
Rwork0.265 5335 -
obs-5618 81.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3acetate.top

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