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- PDB-3dkv: Crystal structure of adenylate kinase variant AKlse1 -

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Basic information

Entry
Database: PDB / ID: 3dkv
TitleCrystal structure of adenylate kinase variant AKlse1
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 / molecular replacement / Resolution: 1.82 Å
AuthorsBannen, R.M. / Bianchetti, C.M. / Bingman, C.A. / Bitto, E.B.
CitationJournal: To be Published
Title: Crystal structure of adenylate kinase variant AKlse1.
Authors: Bannen, R.M. / Bae, E. / McCoy, J.G. / Phillips Jr., G.N.
History
DepositionJun 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 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_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.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.value / _struct_conn.pdbx_dist_value / _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

Downloads & links

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Assembly

Deposited unit
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3397
Polymers24,1471
Non-polymers1,1926
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.624, 62.056, 86.995
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 24146.609 Da / Num. of mol.: 1
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

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Non-polymers , 5 types, 212 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


Mass: 916.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29N10O22P5
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.49 Å3/Da / Density % sol: 50.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 25% PEG 4000, 400mM NaCl, 100 mM Na Acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97297 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97297 Å / Relative weight: 1
ReflectionResolution: 1.69→50.51 Å / Num. obs: 26423 / % possible obs: 95 %
Reflection shellResolution: 1.69→1.75 Å

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.431 / Cor.coef. Fo:Fc: 0.507
Highest resolutionLowest resolution
Rotation3.5 Å25.48 Å
Translation3.5 Å25.48 Å

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1AKY

1aky


Resolution: 1.82→25.47 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.867 / SU B: 4.765 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1145 5.1 %RANDOM
Rwork0.174 ---
obs0.177 22301 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.86 Å2 / Biso mean: 16.918 Å2 / Biso min: 6.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2---0.69 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.82→25.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1687 0 71 206 1964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221786
X-RAY DIFFRACTIONr_angle_refined_deg1.5822.042419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3325218
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68925.1979
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99415322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7231512
X-RAY DIFFRACTIONr_chiral_restr0.1030.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021304
X-RAY DIFFRACTIONr_nbd_refined0.2090.2863
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21236
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2157
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.217
X-RAY DIFFRACTIONr_mcbond_it0.7751.51118
X-RAY DIFFRACTIONr_mcangle_it1.06721743
X-RAY DIFFRACTIONr_scbond_it1.9173759
X-RAY DIFFRACTIONr_scangle_it2.8524.5675
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 98 -
Rwork0.236 1518 -
all-1616 -
obs--98.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.38151.134-0.97913.741-3.15117.22860.01580.109-0.0273-0.2732-0.1767-0.05610.09110.33160.1609-0.01490.0031-0.0204-0.0214-0.00920.01-13.2403-12.2159-13.3579
22.78893.2574-4.136.1136-5.29018.95680.02580.00440.10590.07350.05610.2085-0.4676-0.072-0.08190.0374-0.0008-0.02560.05940.01820.055-21.6208-7.0756-11.5173
34.3682.13110.09431.7455-0.94232.2935-0.2321-0.21640.1954-0.0192-0.093-0.0673-0.52270.10410.32510.108-0.0291-0.07130.03720.01780.1068-12.5093-4.7395-5.028
417.3787-2.4091-1.168115.47573.217719.0709-0.2358-0.76820.81211.1711-0.3407-0.5416-1.3660.41580.57660.5379-0.2678-0.26130.1590.06430.274-1.60726.4488-1.8002
55.1462-5.61991.165911.4452-5.28995.4173-0.34680.42540.63760.2956-0.3062-0.7032-0.86820.85960.6530.1887-0.2273-0.13680.240.17380.28860.76192.731-12.5273
66.52560.13110.75932.8229-1.84767.9971-0.3682-0.06060.37710.17880.0125-0.0374-0.4223-0.03210.35570.0379-0.014-0.06040.06510.02110.0988-4.3918-9.7447-0.2159
79.12331.5134-0.81233.8416-2.37575.9606-0.1206-0.635-0.21490.01110.0532-0.0352-0.01880.03050.06750.02190.0014-0.00750.09130.02240.0702-13.7954-13.5936-3.4875
81.1186-1.25241.50836.0666-2.86215.93680.04290.48510.0605-0.2994-0.2214-0.3155-0.06020.62850.1785-0.0086-0.0050.00470.17110.03070.0904-1.969-14.6074-10.2036
92.5241-1.4083.33622.1645-0.97934.97330.15320.0386-0.1134-0.1561-0.0511-0.06870.19410.2585-0.10210.0292-0.00910.02190.04120.01180.0719-11.0354-18.0188-11.0487
104.2066-2.2773-2.15919.3437-4.991710.1767-0.02760.37840.0857-0.4395-0.225-0.26960.33660.09530.25270.1168-0.0209-0.03160.06850.04740.0609-15.67072.2951-25.0017
113.4596-0.35470.48851.83970.18866.8862-0.0969-0.39720.22610.43560.1830.0537-0.68-0.4586-0.08620.32070.1145-0.00780.08880.01620.0489-25.22187.3566-11.8055
123.366-2.7116-1.11944.43470.38483.8841-0.00970.28970.6693-0.0165-0.219-0.5953-0.52520.32890.22870.1568-0.1119-0.0780.11880.12470.1912-7.7854.4727-19.611
1311.40792.487-1.68448.25-10.128312.61010.03940.5721-0.1974-0.9611-0.0721-0.26211.07110.70180.03270.25720.10730.06390.2421-0.02920.0586-4.6379-17.3979-20.3625
146.0428-3.15443.17146.5667-2.12995.6170.22370.3585-0.2591-0.7187-0.09560.23930.40490.1648-0.1280.1518-0.056-0.03870.03990.01420.0408-18.5648-13.7919-20.9196
155.2877-4.33563.363111.1731-6.29199.0427-0.1141-0.0187-0.41220.1190.32590.64460.2233-0.3083-0.21180.0306-0.0511-0.02730.0835-0.00080.1016-24.3661-17.9528-13.6886
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 91 - 9
2X-RAY DIFFRACTION2AA10 - 2310 - 23
3X-RAY DIFFRACTION3AA24 - 3824 - 38
4X-RAY DIFFRACTION4AA39 - 4939 - 49
5X-RAY DIFFRACTION5AA50 - 6150 - 61
6X-RAY DIFFRACTION6AA62 - 7662 - 76
7X-RAY DIFFRACTION7AA77 - 8577 - 85
8X-RAY DIFFRACTION8AA86 - 10086 - 100
9X-RAY DIFFRACTION9AA101 - 115101 - 115
10X-RAY DIFFRACTION10AA116 - 127116 - 127
11X-RAY DIFFRACTION11AA128 - 156128 - 156
12X-RAY DIFFRACTION12AA157 - 178157 - 178
13X-RAY DIFFRACTION13AA179 - 188179 - 188
14X-RAY DIFFRACTION14AA189 - 202189 - 202
15X-RAY DIFFRACTION15AA203 - 217203 - 217

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