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- PDB-4typ: Crystal structure of an adenylate kinase mutant--AKm1 -

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Basic information

Entry
Database: PDB / ID: 4typ
TitleCrystal structure of an adenylate kinase mutant--AKm1
ComponentsAdenylate kinase
KeywordsTRANSFERASE / adenylate kinase / ATP binding
Function / homology
Function and homology information


nucleoside monophosphate metabolic process / nucleoside diphosphate metabolic process / adenylate kinase / AMP kinase activity / AMP salvage / nucleoside diphosphate kinase activity / zinc ion binding / ATP binding / cytoplasm / cytosol
Similarity search - Function
Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / Adenylate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase ...Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / Adenylate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BIS(ADENOSINE)-5'-PENTAPHOSPHATE / Adenylate kinase
Similarity search - Component
Biological speciesBacillus subtilis 168 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMoon, S. / Bae, E.
CitationJournal: J KOREAN SOC APPL BIOL CHEM / Year: 2014
Title: Crystal structures of thermally stable adenylate kinase mutants designed by local structural entropy optimization and structure-guided mutagenesis
Authors: Moon, S. / Bae, E.
History
DepositionJul 9, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)101,62110
Polymers97,8254
Non-polymers3,7966
Water23413
1
C: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3732
Polymers24,4561
Non-polymers9161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-3 kcal/mol
Surface area10220 Å2
MethodPISA
2
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4383
Polymers24,4561
Non-polymers9822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-5 kcal/mol
Surface area10500 Å2
MethodPISA
3
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4383
Polymers24,4561
Non-polymers9822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-2 kcal/mol
Surface area10790 Å2
MethodPISA
4
D: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3732
Polymers24,4561
Non-polymers9161
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1560 Å2
ΔGint-5 kcal/mol
Surface area9870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.641, 123.338, 86.693
Angle α, β, γ (deg.)90.00, 98.28, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 212
2010B1 - 212
1020A1 - 212
2020C1 - 212
1030A1 - 212
2030D1 - 212
1040B1 - 212
2040C1 - 212
1050B1 - 212
2050D1 - 212
1060C1 - 213
2060D1 - 213

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#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: 24456.176 Da / Num. of mol.: 4
Mutation: L3I, G17A, R19K, E22A, D23K, K69R, G73S, D75S, Y103M, K105R, P106K, I107L, D108E, Y109H, N112H, D106R, K107Q, D108E, V109E, S169A, T179M, Q180K, D184A, S187D, E188S, G190E, Y191V, A193R, ...Mutation: L3I, G17A, R19K, E22A, D23K, K69R, G73S, D75S, Y103M, K105R, P106K, I107L, D108E, Y109H, N112H, D106R, K107Q, D108E, V109E, S169A, T179M, Q180K, D184A, S187D, E188S, G190E, Y191V, A193R, Q198E, I201M, Q202E, D203K, Y205F, A206K, V208L, K209R, D210E, G213Q, K216A, K217R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis 168 (bacteria) / Gene: adk, BSU01370 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P16304, adenylate kinase
#2: Chemical
ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


Mass: 916.367 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H29N10O22P5
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.36 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 18% (w/v) polyethylene glycol 3350, 100mM lithium sulfate, 100mM Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 20, 2014
RadiationMonochromator: DCM Si (111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 20201 / Num. obs: 18989 / % possible obs: 94 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.164 / Net I/σ(I): 5.9
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 2.3 / % possible all: 94.1

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MKG

4mkg


Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.862 / Cor.coef. Fo:Fc free: 0.808 / SU B: 77.842 / SU ML: 0.641 / Cross valid method: THROUGHOUT / ESU R Free: 0.597 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32879 969 5.1 %RANDOM
Rwork0.28755 ---
obs0.28977 17949 93.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.461 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å2-0.72 Å2
2---0.38 Å20 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6261 0 230 13 6504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196591
X-RAY DIFFRACTIONr_bond_other_d0.0020.026397
X-RAY DIFFRACTIONr_angle_refined_deg1.3032.048900
X-RAY DIFFRACTIONr_angle_other_deg2.885314764
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4175777
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.00224.448299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.815151244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9121553
X-RAY DIFFRACTIONr_chiral_restr0.0580.2984
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217111
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021366
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8974.0223147
X-RAY DIFFRACTIONr_mcbond_other1.8974.0223146
X-RAY DIFFRACTIONr_mcangle_it3.1936.0193911
X-RAY DIFFRACTIONr_mcangle_other3.1936.0193912
X-RAY DIFFRACTIONr_scbond_it1.7474.5793444
X-RAY DIFFRACTIONr_scbond_other1.7464.5813445
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0016.8374990
X-RAY DIFFRACTIONr_long_range_B_refined7.65839.14625996
X-RAY DIFFRACTIONr_long_range_B_other7.65739.14825997
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A108480.19
12B108480.19
21A107890.2
22C107890.2
31A104100.21
32D104100.21
41B115840.21
42C115840.21
51B104820.21
52D104820.21
61C105590.22
62D105590.22
LS refinement shellResolution: 2.898→2.973 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.452 61 -
Rwork0.357 1281 -
obs--92.74 %
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)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
10.6447-0.2170.18150.4516-0.46692.07910.0482-0.05340.15690.02150.00270.0120.3160.0968-0.05090.1150.07970.03820.4447-0.00340.0724chain A5.047716.367386.901
21.2182-0.3467-0.39281.6161-0.51221.3624-0.0160.10660.1513-0.19730.0231-0.07580.1305-0.0528-0.00710.11430.00030.03390.35920.01420.0311chain B-4.428121.2273122.3923
31.96510.1866-0.39851.00470.1983.06180.14980.02310.1109-0.12310.1119-0.0657-0.52220.0396-0.26170.1026-0.01310.05320.4023-0.08070.0422chain C-16.2014-23.3434108.3006
40.9646-0.8582-0.50372.25031.42582.5679-0.1394-0.15250.041-0.02780.299-0.1913-0.11130.1382-0.15970.075-0.03880.03430.3485-0.04450.0334chain D8.2141-3.8119147.2556
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1C1 - 212
2X-RAY DIFFRACTION2B1 - 212
3X-RAY DIFFRACTION3A1 - 213
4X-RAY DIFFRACTION4D1 - 214

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