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- PDB-1xmp: Crystal Structure of PurE (BA0288) from Bacillus anthracis at 1.8... -

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Basic information

Entry
Database: PDB / ID: 1xmp
TitleCrystal Structure of PurE (BA0288) from Bacillus anthracis at 1.8 Resolution
Componentsphosphoribosylaminoimidazole carboxylase
KeywordsLYASE / PurE / purine biosynthesis / BA0288 / Bacillus anthracis / SPINE
Function / homology
Function and homology information


5-(carboxyamino)imidazole ribonucleotide mutase / 5-(carboxyamino)imidazole ribonucleotide mutase activity / 'de novo' IMP biosynthetic process / lyase activity
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 / N5-carboxyaminoimidazole ribonucleotide mutase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBoyle, M.P. / Kalliomaa, A.K. / Levdikov, V. / Blagova, E. / Fogg, M.J. / Brannigan, J.A. / Wilkinson, A.J. / Wilson, K.S.
CitationJournal: Proteins / Year: 2005
Title: Crystal structure of PurE (BA0288) from Bacillus anthracis at 1.8 A resolution
Authors: Boyle, M.P. / Kalliomaa, A.K. / Levdikov, V. / Blagova, E. / Fogg, M.J. / Brannigan, J.A. / Wilson, K.S. / Wilkinson, A.J.
History
DepositionOct 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: phosphoribosylaminoimidazole carboxylase
B: phosphoribosylaminoimidazole carboxylase
C: phosphoribosylaminoimidazole carboxylase
D: phosphoribosylaminoimidazole carboxylase
E: phosphoribosylaminoimidazole carboxylase
F: phosphoribosylaminoimidazole carboxylase
G: phosphoribosylaminoimidazole carboxylase
H: phosphoribosylaminoimidazole carboxylase


Theoretical massNumber of molelcules
Total (without water)144,9668
Polymers144,9668
Non-polymers00
Water21,9601219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29170 Å2
ΔGint-184 kcal/mol
Surface area40800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.263, 76.484, 102.675
Angle α, β, γ (deg.)90.00, 96.68, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
phosphoribosylaminoimidazole carboxylase / purE


Mass: 18120.736 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: purE / Plasmid: pET-YSBLIC / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q81ZH8, UniProt: A0A6L7HA71*PLUS, phosphoribosylaminoimidazole carboxylase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1219 / 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: 2.4 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 4000, sodium formate, TRIS, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 30, 2004 / Details: Rh coated Si mirror
RadiationMonochromator: Si monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 120128 / Num. obs: 120128 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 17.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 2.5 / Num. unique all: 11473 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QCZ

1qcz


Resolution: 1.8→31.14 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.563 / SU ML: 0.08 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.119 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20549 5996 5 %RANDOM
Rwork0.16738 ---
all0.1693 113681 --
obs0.1693 113681 50 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→31.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9448 0 0 1219 10667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0229604
X-RAY DIFFRACTIONr_bond_other_d0.0020.029075
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.97613013
X-RAY DIFFRACTIONr_angle_other_deg0.822321101
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.92451262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35224.525358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.783151651
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5071548
X-RAY DIFFRACTIONr_chiral_restr0.0770.21527
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210690
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021734
X-RAY DIFFRACTIONr_nbd_refined0.2050.22207
X-RAY DIFFRACTIONr_nbd_other0.1820.29218
X-RAY DIFFRACTIONr_nbtor_refined0.1640.24812
X-RAY DIFFRACTIONr_nbtor_other0.0830.25196
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2917
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.240.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.931.58119
X-RAY DIFFRACTIONr_mcbond_other0.1761.52623
X-RAY DIFFRACTIONr_mcangle_it1.089210045
X-RAY DIFFRACTIONr_scbond_it2.19633715
X-RAY DIFFRACTIONr_scangle_it3.034.52968
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 444 -
Rwork0.234 8274 -
obs-5996 100 %

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