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- PDB-6zjd: Crystal structure of human adenylate kinase 3, AK3, in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6zjd
TitleCrystal structure of human adenylate kinase 3, AK3, in complex with inhibitor ATP
ComponentsGTP:AMP phosphotransferase AK3, mitochondrial
KeywordsTRANSFERASE / GTP:AMP PHOSPHOTRANSFERASE / Gp5A
Function / homology
Function and homology information


nucleoside-triphosphate-adenylate kinase / ITP metabolic process / UTP metabolic process / nucleoside triphosphate adenylate kinase activity / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / GTP metabolic process / ligase activity / blood coagulation ...nucleoside-triphosphate-adenylate kinase / ITP metabolic process / UTP metabolic process / nucleoside triphosphate adenylate kinase activity / AMP metabolic process / ADP biosynthetic process / nucleoside triphosphate biosynthetic process / GTP metabolic process / ligase activity / blood coagulation / Factors involved in megakaryocyte development and platelet production / mitochondrial matrix / GTP binding / mitochondrion / ATP binding / cytoplasm
Similarity search - Function
Adenylate kinase 3/4, mitochondrial / Adenylate kinase, active site lid domain superfamily / 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
ADENOSINE-5'-TRIPHOSPHATE / GTP:AMP phosphotransferase AK3, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsGrundstrom, C. / Rogne, P. / Wolf-Watz, M. / Sauer-Eriksson, A.E.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Biochemistry / Year: 2020
Title: Structural Basis for GTP versus ATP Selectivity in the NMP Kinase AK3.
Authors: Rogne, P. / Dulko-Smith, B. / Goodman, J. / Rosselin, M. / Grundstrom, C. / Hedberg, C. / Nam, K. / Sauer-Eriksson, A.E. / Wolf-Watz, M.
History
DepositionJun 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTP:AMP phosphotransferase AK3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3089
Polymers25,5991
Non-polymers7088
Water7,566420
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-56 kcal/mol
Surface area11750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.524, 62.518, 49.804
Angle α, β, γ (deg.)90.000, 108.200, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein GTP:AMP phosphotransferase AK3, mitochondrial / Adenylate kinase 3 / AK 3 / Adenylate kinase 3 alpha-like 1


Mass: 25599.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AK3, AK3L1, AK6, AKL3L / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UIJ7, nucleoside-triphosphate-adenylate kinase

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Non-polymers , 5 types, 428 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.46 Å3/Da / Density % sol: 49.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Purified hAK3 was dialyzed against 30 mM MOPS buffer with 50 mM NaCl pH 7.0 and concentrated to 15-20 mg per ml. The resevoir contained 0.2 M MgCl2, 0.1 M Tris pH 8.0 and 20% PEG 6000. Drop ...Details: Purified hAK3 was dialyzed against 30 mM MOPS buffer with 50 mM NaCl pH 7.0 and concentrated to 15-20 mg per ml. The resevoir contained 0.2 M MgCl2, 0.1 M Tris pH 8.0 and 20% PEG 6000. Drop size 1 plus 1 microliter. Cryo protection 30% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Mar 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→26.856 Å / Num. obs: 45601 / % possible obs: 96.2 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.023 / Net I/σ(I): 22.3
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 2335 / CC1/2: 0.887 / Rpim(I) all: 0.203 / % possible all: 79.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1zd8

1zd8


Resolution: 1.75→26.856 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2195 2289 5.02 %
Rwork0.1568 43312 -
obs0.1599 45601 92.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.26 Å2 / Biso mean: 19.8649 Å2 / Biso min: 5.15 Å2
Refinement stepCycle: final / Resolution: 1.75→26.856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1713 0 69 432 2214
Biso mean--25.15 29.54 -
Num. residues----214
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7501-1.78820.32121220.283221375
1.7882-1.82970.29311210.2433231281
1.8297-1.87550.2641380.2112251485
1.8755-1.92620.23171300.1834254287
1.9262-1.98290.23661420.1754259390
1.9829-2.04680.20051350.1703264791
2.0468-2.120.25671430.152270493
2.12-2.20480.22811450.1552274394
2.2048-2.30510.19911470.1544276895
2.3051-2.42650.22521470.1523284297
2.4265-2.57850.24221550.1579291199
2.5785-2.77740.25131530.15632909100
2.7774-3.05650.23661540.15482923100
3.0565-3.4980.20551550.14092915100
3.498-4.40390.17741540.12812906100
4.4039-26.8560.18711480.1497287098

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