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- PDB-9l14: Crystal structure of the monobody CL-1 in complex with the Escher... -

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Basic information

Entry
Database: PDB / ID: 9l14
TitleCrystal structure of the monobody CL-1 in complex with the Escherichia coli adenylate kinase
Components
  • Adenylate kinase
  • Monobody CL-1
KeywordsPROTEIN BINDING / monobody / adenylate kinase / conformational change
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
BIS(ADENOSINE)-5'-PENTAPHOSPHATE / Adenylate kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsNakamura, I. / Amesaka, H. / Tanaka, S.I. / Matsuo, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP22K05316 Japan
CitationJournal: Febs Lett. / Year: 2025
Title: Binding mechanism of adenylate kinase-specific monobodies.
Authors: Nakamura, I. / Amesaka, H. / Nagao, S. / Orito, N. / Negi, S. / Tanaka, S.I. / Matsuo, T.
History
DepositionDec 13, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenylate kinase
B: Monobody CL-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0964
Polymers33,1562
Non-polymers9412
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.530, 63.530, 128.910
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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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.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: adk, dnaW, plsA, b0474, JW0463 / Production host: Escherichia coli HB101 (bacteria) / References: UniProt: P69441, adenylate kinase
#2: Antibody Monobody CL-1


Mass: 9535.536 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical ChemComp-AP5 / BIS(ADENOSINE)-5'-PENTAPHOSPHATE


Mass: 916.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29N10O22P5 / Feature type: SUBJECT OF INVESTIGATION
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.26 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M HEPES buffer pH 7.5, 10% (v/v) 2-propanol, 20% (w/v) polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→31.76 Å / Num. obs: 32927 / % possible obs: 99.9 % / Redundancy: 2 % / CC1/2: 0.998 / Net I/σ(I): 11.43
Reflection shellResolution: 1.69→1.79 Å / Num. unique obs: 5172 / CC1/2: 0.576

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→31.76 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 23.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2354 2985 6.12 %
Rwork0.1915 --
obs0.1942 24699 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.86→31.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2314 0 58 96 2468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082416
X-RAY DIFFRACTIONf_angle_d1.0473290
X-RAY DIFFRACTIONf_dihedral_angle_d23.08336
X-RAY DIFFRACTIONf_chiral_restr0.059377
X-RAY DIFFRACTIONf_plane_restr0.006416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.890.37721360.2632205X-RAY DIFFRACTION100
1.89-1.920.29321440.24112213X-RAY DIFFRACTION100
1.92-1.960.25891360.22622143X-RAY DIFFRACTION100
1.96-20.27141440.20932214X-RAY DIFFRACTION100
2-2.040.28661400.20352192X-RAY DIFFRACTION100
2.04-2.080.27011340.20082169X-RAY DIFFRACTION100
2.08-2.130.22321400.18662182X-RAY DIFFRACTION100
2.13-2.180.25111480.19062217X-RAY DIFFRACTION100
2.18-2.240.28211460.20042157X-RAY DIFFRACTION100
2.24-2.310.2531420.20462152X-RAY DIFFRACTION100
2.31-2.380.22911400.20332219X-RAY DIFFRACTION100
2.38-2.470.29841460.21212159X-RAY DIFFRACTION100
2.47-2.570.22261320.21422192X-RAY DIFFRACTION100
2.57-2.680.21471360.20282216X-RAY DIFFRACTION100
2.68-2.820.29751400.21312169X-RAY DIFFRACTION100
2.82-30.26371540.20592159X-RAY DIFFRACTION100
3-3.230.25221450.1982164X-RAY DIFFRACTION100
3.23-3.550.22811500.18752186X-RAY DIFFRACTION100
3.56-4.070.22961400.1662176X-RAY DIFFRACTION100
4.07-5.120.18691460.16742162X-RAY DIFFRACTION99
5.13-31.760.19351460.1752162X-RAY DIFFRACTION99

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