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- PDB-2osb: Crystal structure of a thermostable mutant of Bacillus subtilis A... -

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Basic information

Entry
Database: PDB / ID: 2osb
TitleCrystal structure of a thermostable mutant of Bacillus subtilis Adenylate Kinase (Q16L/Q199R/)
ComponentsAdenylate kinase
KeywordsTRANSFERASE / thermostability / adenylate kinase / experimental adaptive evolution / directed evolution
Function / homology
Function and homology information


nucleoside monophosphate metabolic process / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage / nucleoside diphosphate kinase activity / phosphorylation / zinc ion binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold ...Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BIS(ADENOSINE)-5'-PENTAPHOSPHATE / Adenylate kinase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMyers, J. / Counago, R. / Wilson, C.J. / Wu, G. / Shamoo, Y.
CitationJournal: To be Published
Title: Crystal structure of a thermostable mutant of Bacillus subtilis Adenylate Kinase (Q16L/Q199R/)
Authors: Counago, R. / Wilson, C.J. / Myers, J. / Wu, G. / Shamoo, Y. / Wittung-Stafshede, P.
History
DepositionFeb 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
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_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
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: Adenylate kinase
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0778
Polymers48,0652
Non-polymers2,0126
Water4,990277
1
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0384
Polymers24,0321
Non-polymers1,0063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0384
Polymers24,0321
Non-polymers1,0063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.578, 74.317, 77.418
Angle α, β, γ (deg.)90.00, 100.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Adenylate kinase / / ATP-AMP transphosphorylase / AK / Superoxide-inducible protein 16 / SOI16


Mass: 24032.314 Da / Num. of mol.: 2 / Mutation: Q16L, Q199R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: adk / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P16304, adenylate kinase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


Mass: 916.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29N10O22P5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.04 Å3/Da / Density % sol: 39.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: CHESS, PEG 1500, CaCl2, pH 9.0, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: May 11, 2006 / Details: mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 45653 / % possible obs: 96.1 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.057 / Χ2: 3.233 / Net I/σ(I): 16.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique all% possible all
1.64-1.71.80.518306565.3
1.7-1.772.50.461464398
1.77-1.852.80.342472799.6
1.85-1.942.90.236472099.8
1.94-2.072.90.157472599.9
2.07-2.2330.114471799.8
2.23-2.4530.086475699.8
2.45-2.830.067473099.7
2.8-3.533.10.047477799.6
3.53-503.10.041479398.8

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Phasing

Phasing MRCor.coef. Fo:Fc: 0.634 / Packing: 0.589
Highest resolutionLowest resolutionMethodReflection percentσ(F)
Translation2 Å15 Ågeneral98.5 0

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2EU8

2eu8


Resolution: 1.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1781 5 %RANDOM
Rwork0.245 ---
obs-34813 97.3 %-
Solvent computationBsol: 30.781 Å2
Displacement parametersBiso mean: 26.726 Å2
Baniso -1Baniso -2Baniso -3
1--7.076 Å20 Å2-4.138 Å2
2--1.928 Å20 Å2
3---5.149 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3364 0 118 277 3759
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1841.5
X-RAY DIFFRACTIONc_scbond_it1.8712
X-RAY DIFFRACTIONc_mcangle_it1.7412
X-RAY DIFFRACTIONc_scangle_it2.7552.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3ap5_xplor_par.txt
X-RAY DIFFRACTION4water_rep.param

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