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- PDB-7apu: Structure of Adenylate kinase from Escherichia coli in complex wi... -

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Basic information

Entry
Database: PDB / ID: 7apu
TitleStructure of Adenylate kinase from Escherichia coli in complex with two ADP molecules refined at 1.36 A resolution.
ComponentsAdenylate kinase
KeywordsTRANSFERASE / PHOSPHOTRANSFERASE / ADENYLATE KINASE / COMPLEX WITH TWO ADP / PROTEIN DYNAMICS
Function / homology
Function and homology information


purine ribonucleotide interconversion / adenine metabolic process / nucleoside monophosphate metabolic process / ADP biosynthetic process / nucleoside diphosphate metabolic process / adenylate kinase / AMP kinase activity / AMP salvage / nucleoside diphosphate kinase activity / AMP binding ...purine ribonucleotide interconversion / adenine metabolic process / nucleoside monophosphate metabolic process / ADP biosynthetic process / nucleoside diphosphate metabolic process / adenylate kinase / AMP 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
ADENOSINE-5'-DIPHOSPHATE / Adenylate kinase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.36 Å
AuthorsGrundstom, C. / Wolf-Watz, M. / Nam, K. / Sauer, U.H.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Biochemistry / Year: 2021
Title: Dynamic Connection between Enzymatic Catalysis and Collective Protein Motions.
Authors: Ojeda-May, P. / Mushtaq, A.U. / Rogne, P. / Verma, A. / Ovchinnikov, V. / Grundstrom, C. / Dulko-Smith, B. / Sauer, U.H. / Wolf-Watz, M. / Nam, K.
History
DepositionOct 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9958
Polymers47,2402
Non-polymers1,7556
Water10,611589
1
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4974
Polymers23,6201
Non-polymers8773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4974
Polymers23,6201
Non-polymers8773
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.754, 82.226, 78.783
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Components on special symmetry positions
IDModelComponents
11B-408-

HOH

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Components

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


Mass: 23620.029 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: adk, dnaW, plsA, b0474, JW0463 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P69441, adenylate kinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 589 / 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: 2.47 Å3/Da / Density % sol: 50 % / Description: rods
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: AdK at 18.3 mg/ml was mixed with 5 mM each of AMP and GTP in 30 mM MOPS buffer pH 7, containing 50 mM NaCl. Hanging drop: 2 ul of AdK, preincubated with AMP and GTP, and 2 ul of precipitant ...Details: AdK at 18.3 mg/ml was mixed with 5 mM each of AMP and GTP in 30 mM MOPS buffer pH 7, containing 50 mM NaCl. Hanging drop: 2 ul of AdK, preincubated with AMP and GTP, and 2 ul of precipitant buffer containing 30% PEG 4000, 0.2 M NH4CH3CO2 (Ammonium Acetate), buffered with 100 mM CH3COONa (Sodium Acetate) adjusted to pH 4.6.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97498 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97498 Å / Relative weight: 1
ReflectionResolution: 1.36→44.81 Å / Num. obs: 99761 / % possible obs: 98.1 % / Redundancy: 7.3 % / Biso Wilson estimate: 16.56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.025 / Rrim(I) all: 0.067 / Net I/σ(I): 14.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.36-1.417.31.0171.995060.6820.3971.09496
5.27-44.816.80.03219220.9980.0130.03598.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimless0.5.15data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AKE

1ake


Resolution: 1.36→44.81 Å / SU ML: 0.163 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.8338
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.206 5028 5.04 %
Rwork0.1843 94693 -
obs0.1854 99721 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.65 Å2
Refinement stepCycle: LAST / Resolution: 1.36→44.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 110 589 4011
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01373559
X-RAY DIFFRACTIONf_angle_d1.56414834
X-RAY DIFFRACTIONf_chiral_restr0.1007537
X-RAY DIFFRACTIONf_plane_restr0.0119623
X-RAY DIFFRACTIONf_dihedral_angle_d18.8035531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.380.34861690.31182995X-RAY DIFFRACTION93.97
1.38-1.390.30721410.30033114X-RAY DIFFRACTION96.79
1.39-1.410.31561710.28093074X-RAY DIFFRACTION96.52
1.41-1.430.311590.26723062X-RAY DIFFRACTION96.24
1.43-1.450.27911710.25973093X-RAY DIFFRACTION97.37
1.45-1.460.23751550.25093079X-RAY DIFFRACTION96.25
1.47-1.490.27691780.23193108X-RAY DIFFRACTION96.93
1.49-1.510.23721530.22663092X-RAY DIFFRACTION97.42
1.51-1.530.23361660.21743103X-RAY DIFFRACTION97.15
1.53-1.560.24441700.21863107X-RAY DIFFRACTION97.36
1.56-1.580.25261570.2143134X-RAY DIFFRACTION97.34
1.58-1.610.2451740.21793113X-RAY DIFFRACTION97.74
1.61-1.640.23091610.20963146X-RAY DIFFRACTION97.87
1.64-1.680.21680.20813139X-RAY DIFFRACTION97.81
1.68-1.710.25461530.20293135X-RAY DIFFRACTION97.11
1.71-1.750.20891680.19223116X-RAY DIFFRACTION97.45
1.75-1.80.2321660.19023130X-RAY DIFFRACTION97.51
1.8-1.850.22021660.19123129X-RAY DIFFRACTION97.98
1.85-1.90.23541690.19093176X-RAY DIFFRACTION98.44
1.9-1.960.23991820.18973167X-RAY DIFFRACTION98.3
1.96-2.030.19191750.18853161X-RAY DIFFRACTION98.87
2.03-2.110.21861900.1953193X-RAY DIFFRACTION99.12
2.11-2.210.20971580.17843161X-RAY DIFFRACTION97.85
2.21-2.330.19491720.17243223X-RAY DIFFRACTION99.39
2.33-2.470.21651630.18053229X-RAY DIFFRACTION99.21
2.47-2.660.23471720.18483239X-RAY DIFFRACTION99.48
2.66-2.930.20021670.18713275X-RAY DIFFRACTION99.42
2.93-3.350.18511800.17373234X-RAY DIFFRACTION98.78
3.35-4.220.16981610.15563334X-RAY DIFFRACTION99.69
4.22-44.810.16051930.1513432X-RAY DIFFRACTION98.94

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