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- PDB-8bqf: Adenylate Kinase L107I MUTANT -

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Basic information

Entry
Database: PDB / ID: 8bqf
TitleAdenylate Kinase L107I MUTANT
ComponentsAdenylate kinase
KeywordsTRANSFERASE / COMPLEX
Function / homology
Function and homology information


purine ribonucleotide interconversion / ADP biosynthetic process / nucleoside monophosphate metabolic process / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage / nucleoside diphosphate kinase activity / AMP binding / magnesium ion binding ...purine ribonucleotide interconversion / ADP biosynthetic process / nucleoside monophosphate metabolic process / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage / nucleoside diphosphate kinase activity / AMP binding / magnesium 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, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / Adenylate kinase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
BIS(ADENOSINE)-5'-PENTAPHOSPHATE / Adenylate kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsScheerer, D. / Adkar, B.V. / Bhattacharyya, S. / Levy, D. / Iljina, M. / Iljina, I. / Dym, O. / Haran, G. / Shakhnovich, E.I.
Funding supportEuropean Union, Israel, 2items
OrganizationGrant numberCountry
European Research Council (ERC)742637European Union
Israel Science Foundation1250/19 Israel
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2023
Title: Allosteric communication between ligand binding domains modulates substrate inhibition in adenylate kinase.
Authors: Scheerer, D. / Adkar, B.V. / Bhattacharyya, S. / Levy, D. / Iljina, M. / Riven, I. / Dym, O. / Haran, G. / Shakhnovich, E.I.
History
DepositionNov 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: 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
C: Adenylate kinase
D: Adenylate kinase
E: Adenylate kinase
F: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,24712
Polymers154,7486
Non-polymers5,4986
Water4,017223
1
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7082
Polymers25,7911
Non-polymers9161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7082
Polymers25,7911
Non-polymers9161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7082
Polymers25,7911
Non-polymers9161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7082
Polymers25,7911
Non-polymers9161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7082
Polymers25,7911
Non-polymers9161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7082
Polymers25,7911
Non-polymers9161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.975, 84.490, 218.493
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein
Adenylate kinase / AK / ATP-AMP transphosphorylase / ATP:AMP phosphotransferase / Adenylate monophosphate kinase


Mass: 25791.402 Da / Num. of mol.: 6 / Mutation: L107I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: adk, dnaW, plsA, b0474, JW0463 / Production host: Escherichia coli (E. coli) / References: UniProt: P69441, adenylate kinase
#2: Chemical
ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


Mass: 916.367 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H29N10O22P5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.33 Å3/Da / Density % sol: 47.11 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 7.5% PEG 3,350, 7.5% PEG 4,000, 7.5% PEG 2,000, 7.5% PEG 5,000 monomethyl ether, 0.07M ammonium nitrate, 2.5% ethylene glycol and 0.05M MES pH=7.
PH range: 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.3405 Å
DetectorType: RIGAKU HyPix-3000 / Detector: PIXEL / Date: Mar 20, 2022
RadiationMonochromator: Ga / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3405 Å / Relative weight: 1
ReflectionResolution: 2.05→21.04 Å / Num. obs: 93318 / % possible obs: 99.69 % / Redundancy: 8.1 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.1043 / Rpim(I) all: 0.03909 / Rrim(I) all: 0.1117 / Net I/σ(I): 20.47
Reflection shellResolution: 2.05→2.123 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.4044 / Mean I/σ(I) obs: 4.39 / Num. unique obs: 8992 / CC1/2: 0.931 / CC star: 0.982 / Rpim(I) all: 0.1585 / Rrim(I) all: 0.435 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7F7U

7f7u
PDB Unreleased entry


Resolution: 2.05→21.04 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.919 / SU B: 4.648 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25789 4792 4.9 %RANDOM
Rwork0.21882 ---
obs0.22073 93318 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.461 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--1.35 Å2-0 Å2
3----1.45 Å2
Refinement stepCycle: 1 / Resolution: 2.05→21.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9486 0 338 223 10047
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01310044
X-RAY DIFFRACTIONr_bond_other_d0.0010.0159444
X-RAY DIFFRACTIONr_angle_refined_deg1.8851.66113718
X-RAY DIFFRACTIONr_angle_other_deg1.3091.58521718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.04451264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.00622.444450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.319151638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.311563
X-RAY DIFFRACTIONr_chiral_restr0.0910.21392
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211171
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022023
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_it2.3612.8835078
X-RAY DIFFRACTIONr_mcbond_other2.362.8825076
X-RAY DIFFRACTIONr_mcangle_it3.5114.3056334
X-RAY DIFFRACTIONr_mcangle_other3.514.3056334
X-RAY DIFFRACTIONr_scbond_it2.6883.0464965
X-RAY DIFFRACTIONr_scbond_other2.6873.0464965
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1474.4527385
X-RAY DIFFRACTIONr_long_range_B_refined5.58633.84410662
X-RAY DIFFRACTIONr_long_range_B_other5.58833.84810627
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.052 Å
RfactorNum. reflection% reflection
Rfree0.328 342 -
Rwork0.271 6856 -
obs--100 %

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