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- PDB-3dl0: Crystal structure of adenylate kinase variant AKlse3 -

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Basic information

Entry
Database: PDB / ID: 3dl0
TitleCrystal structure of adenylate kinase variant AKlse3
ComponentsAdenylate kinase
KeywordsTRANSFERASE / phosphotransferase / zinc coordination / ATP-binding / Kinase / Metal-binding / Nucleotide biosynthesis / Nucleotide-binding
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsBannen, R.M. / Bianchetti, C.M. / Bingman, C.A. / McCoy, J.G.
CitationJournal: Proteins / Year: 2014
Title: Effectiveness and limitations of local structural entropy optimization in the thermal stabilization of mesophilic and thermophilic adenylate kinases.
Authors: Moon, S. / Bannen, R.M. / Rutkoski, T.J. / Phillips, G.N. / Bae, E.
History
DepositionJun 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 25, 2014Group: Database references
Revision 1.3Oct 15, 2014Group: Database references
Revision 1.4Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Aug 30, 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_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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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: Adenylate kinase
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0338
Polymers48,0212
Non-polymers2,0126
Water9,638535
1
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0174
Polymers24,0101
Non-polymers1,0063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0174
Polymers24,0101
Non-polymers1,0063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.003, 76.688, 77.993
Angle α, β, γ (deg.)90.000, 95.300, 90.000
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: 24010.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: gene synthesized by de novo synthesis / Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ADK / Plasmid: pET11 / Production host: Escherichia coli (E. coli) / 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.: 535 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE GENE WAS SYNTHESIZED BY DE NOVO SYNTHESIS. MUTATIONS WERE MADE TO AN ADENYLATE KINASE SEQUENCE ...THE GENE WAS SYNTHESIZED BY DE NOVO SYNTHESIS. MUTATIONS WERE MADE TO AN ADENYLATE KINASE SEQUENCE FROM BACILLUS SUBTILIS TO OPTIMIZE THE PROTEIN'S STRUCTURAL ENTROPY.

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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: 2.11 Å3/Da / Density % sol: 41.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 29% PEG MME 2000, 100mM NaCl, 100mM HEPPS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 9, 2007
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 59416 / % possible obs: 98.9 %
Reflection shellResolution: 1.53→1.58 Å

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DKV

3dkv


Resolution: 1.58→38.84 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.796 / SU B: 2.038 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2758 5.1 %RANDOM
Rwork0.2 ---
obs0.202 54455 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.84 Å2 / Biso mean: 18.394 Å2 / Biso min: 4.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.06 Å2
2---0.32 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.58→38.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3356 0 118 535 4009
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223581
X-RAY DIFFRACTIONr_angle_refined_deg1.5082.0474873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3185448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70525.57158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70415655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7871520
X-RAY DIFFRACTIONr_chiral_restr0.0830.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022634
X-RAY DIFFRACTIONr_nbd_refined0.2070.21800
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22472
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2431
X-RAY DIFFRACTIONr_metal_ion_refined0.0190.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.263
X-RAY DIFFRACTIONr_mcbond_it0.8331.52217
X-RAY DIFFRACTIONr_mcangle_it1.29323493
X-RAY DIFFRACTIONr_scbond_it2.06431526
X-RAY DIFFRACTIONr_scangle_it3.2014.51371
LS refinement shellResolution: 1.58→1.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 219 -
Rwork0.267 3741 -
all-3960 -
obs--97.92 %

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