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- PDB-3qff: Crystal Structure of ADP complex of purK: N5-carboxyaminoimidazol... -

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Basic information

Entry
Database: PDB / ID: 3qff
TitleCrystal Structure of ADP complex of purK: N5-carboxyaminoimidazole ribonucleotide synthetase
ComponentsN5-carboxyaminoimidazole ribonucleotide synthetase
KeywordsLYASE / carboxylase / ATP binding / ADP 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
ADENOSINE-5'-DIPHOSPHATE / :
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsFung, L.W. / Tuntland, M.L. / Santarsiero, B.D. / Johnson, M.E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Elucidation of the bicarbonate binding site and insights into the carboxylation mechanism of (N(5))-carboxyaminoimidazole ribonucleotide synthase (PurK) from Bacillus anthracis.
Authors: Tuntland, M.L. / Santarsiero, B.D. / Johnson, M.E. / Fung, L.W.
History
DepositionJan 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references
Revision 1.2Sep 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 / 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_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

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Assembly

Deposited unit
A: N5-carboxyaminoimidazole ribonucleotide synthetase
B: N5-carboxyaminoimidazole ribonucleotide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2734
Polymers86,4192
Non-polymers8542
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-18 kcal/mol
Surface area29350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.421, 82.089, 166.768
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.27 Å3/Da / Density % sol: 45.91 %
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 C3/27 and 3mM ADP, pH 6.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionHighest resolution: 1.96 Å / Num. obs: 55699 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 39.42 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 14.43
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.96-2.080.8161.9837758743982.1
2.08-2.220.5714.26704948596100
2.22-2.40.3526.76654987976100
2.4-2.620.22210.05607677408100
2.62-2.930.13415.13547116715100
2.93-3.380.08322.83479155972100
3.38-4.110.05830.86396745100100
4.11-5.740.0535.19307664042100
5.740.04335.3517617245198.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3Q2O

3q2o


Resolution: 1.96→19.97 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.2551 / WRfactor Rwork: 0.1987 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.841 / SU B: 4.24 / SU ML: 0.121 / SU R Cruickshank DPI: 0.1901 / SU Rfree: 0.1744 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2515 2832 5.1 %RANDOM
Rwork0.1989 ---
obs0.2015 55669 97.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 68.43 Å2 / Biso mean: 34.6697 Å2 / Biso min: 12.81 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.96→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5876 0 54 317 6247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226044
X-RAY DIFFRACTIONr_angle_refined_deg1.1821.9788209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5385752
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.81125.407270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.506151076
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.741528
X-RAY DIFFRACTIONr_chiral_restr0.0770.2950
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214466
X-RAY DIFFRACTIONr_mcbond_it0.6691.53746
X-RAY DIFFRACTIONr_mcangle_it1.25926046
X-RAY DIFFRACTIONr_scbond_it1.76532298
X-RAY DIFFRACTIONr_scangle_it3.034.52162
LS refinement shellResolution: 1.961→2.012 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 130 -
Rwork0.312 2371 -
all-2501 -
obs--60.66 %

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