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- PDB-5eje: Crystal structure of E. coli Adenylate kinase G56C/T163C double m... -

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Basic information

Entry
Database: PDB / ID: 5eje
TitleCrystal structure of E. coli Adenylate kinase G56C/T163C double mutant in complex with Ap5a
ComponentsAdenylate kinase
KeywordsTRANSFERASE / Adenylate kinase / G56C and T163C variant / disulfide bond / Ap5A ligand
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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase ...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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BIS(ADENOSINE)-5'-PENTAPHOSPHATE / : / Adenylate kinase / Adenylate kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSauer, U.H. / Kovermann, M. / Grundstrom, C. / Wolf-Watz, M. / Sauer-Eriksson, A.E.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council621-2014-4493 Sweden
Swedish Research Council621-2013-5954 Sweden
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural basis for ligand binding to an enzyme by a conformational selection pathway.
Authors: Kovermann, M. / Grundstrom, C. / Sauer-Eriksson, A.E. / Sauer, U.H. / Wolf-Watz, M.
History
DepositionNov 1, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenylate kinase
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2876
Polymers47,3362
Non-polymers1,9514
Water9,944552
1
A: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6433
Polymers23,6681
Non-polymers9752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Adenylate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6433
Polymers23,6681
Non-polymers9752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.003, 79.064, 81.834
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
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: 23668.160 Da / Num. of mol.: 2 / Mutation: G56C and T163C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: E24377A / ETEC / Gene: adk, EcE24377A_0513 / Production host: Escherichia coli (E. coli)
References: UniProt: A7ZIN4, UniProt: P69441*PLUS, adenylate kinase
#2: Chemical ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


Mass: 916.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29N10O22P5
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / 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: 2.49 Å3/Da / Density % sol: 50.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: Purified AdK in 50 mM NaCl and 30 mM MES buffer, pH 6.0 was concentrated to 13 mg/ml and co-crystallized with a 5 molar excess of Ap5a. A typical drop contained 1 microL of protein mixed ...Details: Purified AdK in 50 mM NaCl and 30 mM MES buffer, pH 6.0 was concentrated to 13 mg/ml and co-crystallized with a 5 molar excess of Ap5a. A typical drop contained 1 microL of protein mixed with 1 microL of precipitant and equilibrated against 1 mL reservoir solution containing 26-28% PEG 8K, 10 mM CoCl2 and 0.1 M NaOAc, pH 5.8).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.038 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.038 Å / Relative weight: 1
ReflectionResolution: 1.9→26.8 Å / Num. obs: 37833 / % possible obs: 99.6 % / Redundancy: 14.6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 18.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 14.1 % / Rmerge(I) obs: 1.99 / Mean I/σ(I) obs: 1.8 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX(1.10_2140: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AKE

4ake


Resolution: 1.9→26.8 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / Phase error: 25.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2358 1995 5.28 %
Rwork0.1863 --
obs0.1889 37813 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→26.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3314 0 116 552 3982
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033498
X-RAY DIFFRACTIONf_angle_d0.7564745
X-RAY DIFFRACTIONf_dihedral_angle_d13.5012151
X-RAY DIFFRACTIONf_chiral_restr0.043525
X-RAY DIFFRACTIONf_plane_restr0.004605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9003-1.94780.41331370.3432441X-RAY DIFFRACTION97
1.9478-2.00050.29831370.27712531X-RAY DIFFRACTION99
2.0005-2.05930.31041410.25072500X-RAY DIFFRACTION100
2.0593-2.12580.31981370.23912526X-RAY DIFFRACTION100
2.1258-2.20170.26391510.21672536X-RAY DIFFRACTION100
2.2017-2.28980.26141380.2232545X-RAY DIFFRACTION100
2.2898-2.3940.28551410.19532542X-RAY DIFFRACTION100
2.394-2.52010.26511430.20552531X-RAY DIFFRACTION100
2.5201-2.67790.23121400.20382566X-RAY DIFFRACTION100
2.6779-2.88440.30011430.20062576X-RAY DIFFRACTION100
2.8844-3.17420.25861450.17732574X-RAY DIFFRACTION100
3.1742-3.63260.19931400.16242604X-RAY DIFFRACTION100
3.6326-4.5730.20131480.14882625X-RAY DIFFRACTION100
4.573-26.80.17671540.16052721X-RAY DIFFRACTION99

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