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- PDB-6ln3: Crystal structure of adenylate kinase from an extremophilic archa... -

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Basic information

Entry
Database: PDB / ID: 6ln3
TitleCrystal structure of adenylate kinase from an extremophilic archaeon Aeropyrum pernix with ATP and AMP
ComponentsAdenylate kinase
KeywordsTRANSFERASE / adenylate kinase / ATP / AMP / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


adenylate kinase / AMP kinase activity / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Adenylate kinase AdkA / AAA domain / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / Adenylate kinase
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShibanuma, Y. / Nemoto, N. / Yamamoto, N. / Sampei, G. / Kawai, G.
CitationJournal: J.Biochem. / Year: 2020
Title: Crystal structure of adenylate kinase from an extremophilic archaeon Aeropyrum pernix with ATP and AMP.
Authors: Shibanuma, Y. / Nemoto, N. / Yamamoto, N. / Sampei, G.I. / Kawai, G.
History
DepositionDec 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.2Nov 22, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1346
Polymers21,9821
Non-polymers1,1525
Water2,738152
1
A: Adenylate kinase
hetero molecules

A: Adenylate kinase
hetero molecules

A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,40218
Polymers65,9453
Non-polymers3,45715
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation58_555-y+1/2,z,-x+1/21
crystal symmetry operation79_555-z+1/2,-x+1/2,y1
Buried area10430 Å2
ΔGint-61 kcal/mol
Surface area22640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.440, 193.440, 193.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Components on special symmetry positions
IDModelComponents
11A-552-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 21981.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1) (archaea)
Strain: ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1
Gene: adkA, APE_0981.1 / Plasmid: pET-21a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: Q9YDD2, adenylate kinase

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Non-polymers , 6 types, 157 molecules

#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 3.32 Å3/Da / Density % sol: 62.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.6
Details: 0.2 M Ammonium sulfate, 0.1 M HEPES pH 7.6, 25% (w/v) Polyethylene glycol monomethyl ether 2000, 5 mM adenosine 5'-triphosphate, 5 mM magnesium ions

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 23, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 20843 / % possible obs: 96.9 % / Redundancy: 37.8 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 79.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 25.2 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 11.4 / Num. unique obs: 1679 / % possible all: 80.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.22data extraction
HKL-20001.98.5data reduction
HKL-20001.98.5data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KHT

1kht


Resolution: 2→32.7 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1918 1062 5.1 %RANDOM
Rwork0.1596 ---
obs0.1612 19709 96.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109 Å2 / Biso mean: 24.776 Å2 / Biso min: 13.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2→32.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1543 0 71 152 1766
Biso mean--24.44 34.91 -
Num. residues----202
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0131634
X-RAY DIFFRACTIONr_bond_other_d0.0340.0171620
X-RAY DIFFRACTIONr_angle_refined_deg1.9591.662218
X-RAY DIFFRACTIONr_angle_other_deg2.2861.5963740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9175201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.9320.77977
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2215293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1221515
X-RAY DIFFRACTIONr_chiral_restr0.0990.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021769
X-RAY DIFFRACTIONr_gen_planes_other0.0120.02314
X-RAY DIFFRACTIONr_mcbond_it2.2012.205806
X-RAY DIFFRACTIONr_mcbond_other2.1992.204805
X-RAY DIFFRACTIONr_mcangle_it2.9583.2991007
LS refinement shellResolution: 2.002→2.054 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 67 -
Rwork0.188 1161 -
all-1228 -
obs--79.28 %

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