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- PDB-4cf7: Crystal structure of adenylate kinase from Aquifex aeolicus with ... -

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Basic information

Entry
Database: PDB / ID: 4cf7
TitleCrystal structure of adenylate kinase from Aquifex aeolicus with MgADP bound
ComponentsADENYLATE KINASE
KeywordsTRANSFERASE / PHOSPHORYL TRANSFER / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


nucleoside monophosphate metabolic process / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage / nucleoside diphosphate kinase activity / phosphorylation / intracellular membrane-bounded organelle / ATP binding / cytosol / cytoplasm
Similarity search - Function
Adenylate kinase, active site lid domain superfamily / 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
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE MONOPHOSPHATE / Adenylate kinase
Similarity search - Component
Biological speciesAQUIFEX AEOLICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.594 Å
AuthorsKerns, S.J. / Agafonov, R.V. / Cho, Y.-J. / Pontiggia, F. / Otten, R. / Pachov, D.V. / Kutter, S. / Phung, L.A. / Murphy, P.N. / Thai, V. ...Kerns, S.J. / Agafonov, R.V. / Cho, Y.-J. / Pontiggia, F. / Otten, R. / Pachov, D.V. / Kutter, S. / Phung, L.A. / Murphy, P.N. / Thai, V. / Hagan, M.F. / Kern, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: The Energy Landscape of Adenylate Kinase During Catalysis.
Authors: Kerns, S.J. / Agafonov, R.V. / Cho, Y. / Pontiggia, F. / Otten, R. / Pachov, D.V. / Kutter, S. / Phung, L.A. / Murphy, P.N. / Thai, V. / Alber, T. / Hagan, M.F. / Kern, D.
History
DepositionNov 13, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Jan 21, 2015Group: Database references
Revision 1.3Feb 18, 2015Group: Database references
Revision 1.4Mar 29, 2017Group: Other
Revision 1.5Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.6May 22, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.7Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_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)48,6188
Polymers46,5382
Non-polymers2,0806
Water6,017334
1
A: ADENYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1233
Polymers23,2691
Non-polymers8542
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ADENYLATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4955
Polymers23,2691
Non-polymers1,2264
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.088, 64.697, 86.256
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ADENYLATE KINASE / / AK / ATP-AMP TRANSPHOSPHORYLASE / ATP\:AMP PHOSPHOTRANSFERASE / ADENYLATE MONOPHOSPHATE KINASE


Mass: 23269.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AQUIFEX AEOLICUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O66490, adenylate kinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O

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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: 1.95 Å3/Da / Density % sol: 37.02 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9
Details: A 1.5 UL SOLUTION CONTAINING 26 MG/ML OF PROTEIN, 20 MM MGCL2 AND 20 MM ADP IN 50 MM TRIS-HCL PH 7 WAS MIXED WITH 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM ACETATE TRIHYDRATE PH 5.6, 30% W/V PEG- ...Details: A 1.5 UL SOLUTION CONTAINING 26 MG/ML OF PROTEIN, 20 MM MGCL2 AND 20 MM ADP IN 50 MM TRIS-HCL PH 7 WAS MIXED WITH 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM ACETATE TRIHYDRATE PH 5.6, 30% W/V PEG-4000 IN A 1:1 RATIO; VAPOR DIFFUSION; SITTING DROP; 291 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.00001
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 12, 2013
RadiationMonochromator: DOUBLE CRYSTAL . SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.59→64.7 Å / Num. obs: 48649 / % possible obs: 100 % / Observed criterion σ(I): 3.1 / Redundancy: 6.5 % / Biso Wilson estimate: 15.53 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.2
Reflection shellResolution: 1.59→1.64 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SR0

3sr0


Resolution: 1.594→40.265 Å / SU ML: 0.15 / σ(F): 1.34 / Phase error: 22.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2158 1030 2.1 %
Rwork0.1817 --
obs0.1825 48566 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.8 Å2
Refinement stepCycle: LAST / Resolution: 1.594→40.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3236 0 132 334 3702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073546
X-RAY DIFFRACTIONf_angle_d1.3284834
X-RAY DIFFRACTIONf_dihedral_angle_d18.2611435
X-RAY DIFFRACTIONf_chiral_restr0.05537
X-RAY DIFFRACTIONf_plane_restr0.006600
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5937-1.67770.25371210.22266733X-RAY DIFFRACTION100
1.6777-1.78280.26571440.21156706X-RAY DIFFRACTION100
1.7828-1.92050.23381460.20016707X-RAY DIFFRACTION100
1.9205-2.11380.22131530.18836741X-RAY DIFFRACTION100
2.1138-2.41960.21521570.18126744X-RAY DIFFRACTION100
2.4196-3.04830.2691500.19146851X-RAY DIFFRACTION100
3.0483-40.27830.17091590.15977054X-RAY DIFFRACTION100

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