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- PDB-3q2o: Crystal Structure of purK: N5-carboxyaminoimidazole ribonucleotid... -

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Basic information

Entry
Database: PDB / ID: 3q2o
TitleCrystal Structure of purK: N5-carboxyaminoimidazole ribonucleotide synthetase
ComponentsPhosphoribosylaminoimidazole carboxylase, ATPase subunit
KeywordsLYASE / carboxylase / carboxylates / ATP Binding
Function / homology
Function and homology information


Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.96 Å
AuthorsFung, L.W. / Tuntland, M.L. / Santarsiero, B.D. / Johnson, M.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structure of N(5)-carboxyaminoimidazole ribonucleotide synthase (PurK) from Bacillus anthracis.
Authors: Tuntland, M.L. / Johnson, M.E. / Fung, L.W. / Santarsiero, B.D.
History
DepositionDec 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4674
Polymers86,4192
Non-polymers492
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-25 kcal/mol
Surface area29790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.430, 82.445, 166.621
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is dimer and same as asymmetric unit.

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Components

#1: Protein Phosphoribosylaminoimidazole carboxylase, ATPase subunit / N5-carboxyaminoimidazole ribonucleotide synthetase


Mass: 43209.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: A0248 / Gene: BAA_0344, purK / Plasmid: pDEST15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL
References: UniProt: C3PBM5, phosphoribosylaminoimidazole carboxylase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.28 Å3/Da / Density % sol: 46.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES, 5mM DTT, 9% glycerol, 10% PEG6000, Hampton Research Silver Bullet Bio additive B5/17, pH 6.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 22-ID11
SYNCHROTRONAPS 24-ID-E20.9791
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDDec 2, 2010
ADSC QUANTUM 3152CCDAug 5, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1mirrorsSINGLE WAVELENGTHMx-ray1
2mirrorsSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97911
ReflectionNumber: 131923 / Rmerge(I) obs: 0.139 / D res high: 2.79 Å / D res low: 19.96 Å / Num. obs: 19596 / % possible obs: 95
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
8.219.9691298.210.048
5.878.2147499.910.074
4.815.87183899.910.088
4.184.81214210010.088
3.744.18241299.910.128
3.423.74266110010.204
3.163.42285999.910.329
2.963.16304999.710.515
2.792.96224969.110.612
ReflectionResolution: 1.96→20 Å / Num. all: 56242 / Num. obs: 56242 / % possible obs: 96.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 34.171 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 14.67
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
1.96-2.074.90.752.7368147484748481.3
2.07-2.228.10.5215.57070386858685100
2.22-2.3980.3578.2645638077807799.7
2.39-2.628.20.22111.56125874617461100
2.62-2.928.20.14215.85513567606760100
2.92-3.378.10.08822.14916360626062100
3.37-4.117.80.06628.64009751655163100
4.11-5.737.70.05533315684079407699.9
5.73-19.967.40.0533.2181932518247498.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 57.75 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å19.98 Å
Translation3 Å19.98 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology model of 3K5I

3k5i


Resolution: 1.96→19.96 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2384 / WRfactor Rwork: 0.1936 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8471 / SU B: 3.85 / SU ML: 0.11 / SU R Cruickshank DPI: 0.1845 / SU Rfree: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2352 2848 5.1 %RANDOM
Rwork0.1952 ---
all0.1973 53364 --
obs0.1973 53364 97.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 64.11 Å2 / Biso mean: 28.5343 Å2 / Biso min: 11.21 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.162 Å0.185 Å
Luzzati d res low-19.96 Å
Refinement stepCycle: LAST / Resolution: 1.96→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5876 0 2 379 6257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225976
X-RAY DIFFRACTIONr_angle_refined_deg1.1091.9658102
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3415752
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.20725.407270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.967151076
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7281528
X-RAY DIFFRACTIONr_chiral_restr0.0750.2940
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214452
X-RAY DIFFRACTIONr_mcbond_it0.6551.53748
X-RAY DIFFRACTIONr_mcangle_it1.23326050
X-RAY DIFFRACTIONr_scbond_it1.68632228
X-RAY DIFFRACTIONr_scangle_it2.934.52052
LS refinement shellResolution: 1.957→2.007 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 133 -
Rwork0.282 2451 -
all-2584 -
obs--61.39 %

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