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- PDB-4tyq: Crystal structure of an adenylate kinase mutant--AKm2 -

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Basic information

Entry
Database: PDB / ID: 4tyq
TitleCrystal structure of an adenylate kinase mutant--AKm2
ComponentsAdenylate kinase
KeywordsTRANSFERASE / 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: 1.65 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_conn_angle / pdbx_struct_oper_list / struct_conn
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_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 / _pdbx_struct_oper_list.symmetry_operation / _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_conn.ptnr2_symmetry

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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)50,8649
Polymers48,8122
Non-polymers2,0527
Water5,981332
1
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4525
Polymers24,4061
Non-polymers1,0464
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-4 kcal/mol
Surface area10560 Å2
MethodPISA
2
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,4124
Polymers24,4061
Non-polymers1,0063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-3 kcal/mol
Surface area10630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.003, 48.790, 54.832
Angle α, β, γ (deg.)90.98, 97.34, 95.83
Int Tables number1
Space group name H-MP1

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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: 24406.096 Da / Num. of mol.: 2
Mutation: L3I, G17A, E22A, D23K, K69R, G73S, D75S, Y103M, K105R, P106K, I107L, D108E, N112H, D106R, K107Q, D108E, V109E, S169A, T179M, Q180A, D184A, S187D, E188S, G190E, Y191V, A193V, I201M, Q202E, ...Mutation: L3I, G17A, E22A, D23K, K69R, G73S, D75S, Y103M, K105R, P106K, I107L, D108E, N112H, D106R, K107Q, D108E, V109E, S169A, T179M, Q180A, D184A, S187D, E188S, G190E, Y191V, A193V, I201M, Q202E, D203K, Y205F, A206K, V208L, K209R, D210E, L211I, 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

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Non-polymers , 5 types, 339 molecules

#2: Chemical ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


Mass: 916.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29N10O22P5
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 22% (w/v) polyethylene glycol 3350, 200mM calcium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2014
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 47801 / Num. obs: 45746 / % possible obs: 95.7 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 8.4
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 4.6 / % possible all: 92.3

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZIO

1zio


Resolution: 1.65→50 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.167 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2186 2309 5 %RANDOM
Rwork0.17534 ---
obs0.17747 43435 95.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.729 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å2-0.01 Å2-0.59 Å2
2--0.39 Å2-0.09 Å2
3---0.84 Å2
Refinement stepCycle: 1 / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3369 0 119 332 3820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0193539
X-RAY DIFFRACTIONr_bond_other_d0.0010.023393
X-RAY DIFFRACTIONr_angle_refined_deg2.2462.0364788
X-RAY DIFFRACTIONr_angle_other_deg2.437839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3315428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03224.625160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10515655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8021528
X-RAY DIFFRACTIONr_chiral_restr0.1340.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213886
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02734
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_it1.671.491718
X-RAY DIFFRACTIONr_mcbond_other1.6571.4881717
X-RAY DIFFRACTIONr_mcangle_it2.2712.2332144
X-RAY DIFFRACTIONr_mcangle_other2.2752.2342145
X-RAY DIFFRACTIONr_scbond_it3.3551.9121821
X-RAY DIFFRACTIONr_scbond_other3.3551.9121822
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1132.692645
X-RAY DIFFRACTIONr_long_range_B_refined7.60213.7164258
X-RAY DIFFRACTIONr_long_range_B_other7.55113.0094126
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.651→1.694 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 173 -
Rwork0.192 2989 -
obs--88.65 %
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)
10.0190.10370.02510.84140.50660.8791-0.0034-0.001600.02520.0143-0.03220.05320.0182-0.01090.0086-0.0031-0.00890.0320.01340.017chain A flap region12.2199-15.9314-8.3248
20.0274-0.0553-0.08361.36551.5771.8923-0.0013-0.0077-0.0015-0.1005-0.0110.0144-0.1128-0.01180.01230.02830.00970.00190.00610.00040.0047chain B flap region12.3631-5.3635-18.1752
30.1913-0.0989-0.13070.17630.08760.2239-0.0005-0.00440.01040.01570.0061-0.01270.0217-0.0002-0.00560.0187-0.0006-0.0020.0003-0.00050.0012chain A lid domain12.1366-10.6868-13.131
40.0069-0.01810.02160.0672-0.03310.22810.0095-0.00660.0103-0.01890.0224-0.0395-0.0180.0282-0.03190.07220.00560.01580.08240.00120.0856chain B lid domain12.2574-8.1454-15.715
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 60
2X-RAY DIFFRACTION1B31 - 60
3X-RAY DIFFRACTION2A127 - 164
4X-RAY DIFFRACTION2B127 - 164
5X-RAY DIFFRACTION3A1 - 30
6X-RAY DIFFRACTION3B1 - 30
7X-RAY DIFFRACTION3A61 - 126
8X-RAY DIFFRACTION3B61 - 126
9X-RAY DIFFRACTION3A165 - 215
10X-RAY DIFFRACTION3B165 - 214

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