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- PDB-4x8h: Crystal structure of E. coli Adenylate kinase P177A mutant -

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Basic information

Entry
Database: PDB / ID: 4x8h
TitleCrystal structure of E. coli Adenylate kinase P177A mutant
ComponentsAdenylate kinase
KeywordsTRANSFERASE / Adenylate Kinase / P177A / Apo-form / Protein Dynamics
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 / phosphorylation ...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 / phosphorylation / 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 / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold ...Adenylate kinase, active site lid domain / Adenylate kinase, active site lid / Adenylate kinase subfamily / Adenylate kinase / Adenylate kinase, conserved site / Adenylate kinase signature. / Adenylate kinase/UMP-CMP kinase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSauer-Eriksson, A.E. / Kovermann, M. / Aden, J. / Grundstrom, C. / Wolf-Watz, M. / Sauer, U.H.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Nat Commun / Year: 2015
Title: Structural basis for catalytically restrictive dynamics of a high-energy enzyme state.
Authors: Kovermann, M. / Aden, J. / Grundstrom, C. / Elisabeth Sauer-Eriksson, A. / Sauer, U.H. / Wolf-Watz, M.
History
DepositionDec 10, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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: Adenylate kinase


Theoretical massNumber of molelcules
Total (without water)23,5941
Polymers23,5941
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.418, 31.534, 52.745
Angle α, β, γ (deg.)90.00, 110.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 23593.992 Da / Num. of mol.: 1 / Mutation: P177A
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.23 Å3/Da / Density % sol: 44.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 30% PEG 4K, 0.1 M Tris-HCl, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Feb 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→33.6 Å / Num. obs: 7465 / % possible obs: 98.5 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 16.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.345 / % possible all: 89

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ake

4ake


Resolution: 2.5→33.6 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2895 358 4.8 %
Rwork0.1914 --
obs0.1961 7465 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43 Å2
Refinement stepCycle: LAST / Resolution: 2.5→33.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1654 0 0 150 1804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031677
X-RAY DIFFRACTIONf_angle_d0.6422259
X-RAY DIFFRACTIONf_dihedral_angle_d12.965649
X-RAY DIFFRACTIONf_chiral_restr0.026254
X-RAY DIFFRACTIONf_plane_restr0.002298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.86160.34741050.25562352X-RAY DIFFRACTION100
2.8616-3.60460.32121290.20492350X-RAY DIFFRACTION100
3.6046-33.60.25341240.16322405X-RAY DIFFRACTION99

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