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- PDB-4mkf: Crystal structure of a stable adenylate kinase variant AKv3 -

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Basic information

Entry
Database: PDB / ID: 4mkf
TitleCrystal structure of a stable adenylate kinase variant AKv3
ComponentsAdenylate kinase
KeywordsTRANSFERASE / Adenylate kinase / Zinc Finger / transferase activity / phosphotransferase activity / Zinc binding / ATP binding / Phosphorylation
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: 1.7 Å
AuthorsMoon, S. / Jung, D. / Bae, E.
CitationJournal: Proteins / Year: 2014
Title: An integrated approach for thermal stabilization of a mesophilic adenylate kinase.
Authors: Moon, S. / Jung, D.K. / Phillips Jr., G.N. / Bae, E.
History
DepositionSep 5, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 8, 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

Downloads & links

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Assembly

Deposited unit
A: Adenylate kinase
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,68015
Polymers48,3872
Non-polymers2,29313
Water8,485471
1
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3207
Polymers24,1941
Non-polymers1,1266
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3608
Polymers24,1941
Non-polymers1,1667
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.447, 75.008, 77.195
Angle α, β, γ (deg.)90.00, 100.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 24193.553 Da / Num. of mol.: 2 / Mutation: R19K, D116R, T179M, Q198E, Q202E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: adk, BSU01370 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P16304, adenylate kinase

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Non-polymers , 5 types, 484 molecules

#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: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.02 Å3/Da / Density % sol: 39.23 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 36% (w/v) polyethylene glycol 1500, 50mM CaCl2, 50mM Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 13, 2010
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 42304 / Num. obs: 42262 / % possible obs: 99.9 % / Observed criterion σ(I): -3
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 4.4 / Num. unique all: 4194 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1P3J

1p3j


Resolution: 1.7→26.99 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.001 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20271 2131 5 %RANDOM
Rwork0.15674 ---
obs0.15904 42262 99.82 %-
all-42304 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.005 Å2
Baniso -1Baniso -2Baniso -3
1-0.83 Å20 Å20.89 Å2
2---0.32 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.7→26.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3384 0 125 471 3980
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.023558
X-RAY DIFFRACTIONr_angle_refined_deg2.2532.0454822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6995432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23325.5160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16515646
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0551520
X-RAY DIFFRACTIONr_chiral_restr0.150.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212630
LS refinement shellResolution: 1.702→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 162 -
Rwork0.189 2836 -
obs--98.59 %
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)
11.9739-0.06640.09391.31960.46023.83010.01190.0819-0.0259-0.1295-0.0466-0.0551-0.1147-0.10990.03480.04540.01730.01470.0377-0.00260.00818.92234.826-0.9368
22.97142.01350.43622.22210.35591.4770.00990.17670.0491-0.04240.00390.15410.030.004-0.01370.03280.0193-0.01090.0314-0.01450.01880.3052-13.9126-0.6946
30.5477-0.1475-0.15720.41320.19110.78940.0339-0.0283-0.0306-0.0220.0003-0.01490.00610.0458-0.03420.00750.0039-0.00020.00820.00190.00575.9867-1.756216.2848
40.1341-0.56110.15992.6776-0.05951.41920.02580.01350.0098-0.01940.0097-0.08530.11870.0684-0.03550.0460.02950.00770.0587-0.00660.0557.8445-6.74477.4644
50.9757-0.29730.10171.305-0.89752.45960.00980.01280.08910.0045-0.0315-0.033-0.16210.03660.02170.0268-0.00370.00010.0098-0.00240.00991.67925.068337.2523
61.99931.4325-0.31313.8197-0.63211.45870.00620.10310.03370.05250.06450.25870.0969-0.0041-0.07060.01650.0060.00270.00910.00020.0246-7.1657-13.790435.6524
70.45130.00040.02350.50590.05510.941-0.0072-0.06480.02680.05740.02350.0313-0.03840.0199-0.01620.01150.0067-0.00010.0165-0.00860.0114-0.9802-3.514153.9104
80.0231-0.0791-0.12160.7003-0.25361.8396-0.0196-0.0210.01580.04880.1152-0.09040.08230.0963-0.09560.07210.01340.00860.0837-0.00540.08070.5063-7.404244.4475
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 60
2X-RAY DIFFRACTION2A127 - 164
3X-RAY DIFFRACTION3A1 - 30
4X-RAY DIFFRACTION3A61 - 126
5X-RAY DIFFRACTION3A165 - 217
6X-RAY DIFFRACTION4A303
7X-RAY DIFFRACTION5B31 - 60
8X-RAY DIFFRACTION6B127 - 164
9X-RAY DIFFRACTION7B1 - 30
10X-RAY DIFFRACTION7B61 - 126
11X-RAY DIFFRACTION7B165 - 217
12X-RAY DIFFRACTION8B303

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