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

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Basic information

Entry
Database: PDB / ID: 2fwi
TitleStructure of PurE (N5-carboxyaminoimidazole ribonucleotide mutase) H59D, from the acidophilic bacterium Acetobacter aceti, complexed with 5-aminoimidazole ribonucleotide (AIR)
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
5-AMINOIMIDAZOLE RIBONUCLEOTIDE / N5-carboxyaminoimidazole ribonucleotide mutase
Similarity search - Component
Biological speciesAcetobacter aceti (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.94 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 2, 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: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0143
Polymers37,7192
Non-polymers2951
Water5,134285
1
A: N5-carboxyaminoimidazole ribonucleotide mutase
B: N5-carboxyaminoimidazole ribonucleotide mutase
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)152,05812
Polymers150,8778
Non-polymers1,1814
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
Unit cell
Length a, b, c (Å)99.046, 99.046, 163.829
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: 18859.650 Da / Num. of mol.: 2 / Mutation: H59D
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: Chemical ChemComp-AIR / 5-AMINOIMIDAZOLE RIBONUCLEOTIDE


Mass: 295.186 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14N3O7P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.66 Å3/Da / Density % sol: 53.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M lithium sulfate, 0.1M Tris pH 8, 30% (w/v) PEG 4000 (soaked at pH 7), 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: Dec 9, 2005
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. obs: 30234 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rsym value: 0.066 / Net I/σ(I): 22.7
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 5 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 2969 / Rsym value: 0.518 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1U11

1u11


Resolution: 1.94→40 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.508 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19088 1440 5 %RANDOM
Rwork0.16385 ---
obs0.16519 27638 95.64 %-
all-30234 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.367 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2---0.27 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.94→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2321 0 19 285 2625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222385
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.31.9953265
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8495318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.40622.98777
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.99815367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7941519
X-RAY DIFFRACTIONr_chiral_restr0.0840.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021766
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.21232
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21685
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2232
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.298
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7871.51639
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36922547
X-RAY DIFFRACTIONr_scbond_it2.2983846
X-RAY DIFFRACTIONr_scangle_it3.4324.5718
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.943→1.993 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 93 -
Rwork0.215 1789 -
obs-1882 85.43 %

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