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- PDB-3loo: Crystal structure of Anopheles gambiae adenosine kinase in comple... -

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Basic information

Entry
Database: PDB / ID: 3loo
TitleCrystal structure of Anopheles gambiae adenosine kinase in complex with P1,P4-di(adenosine-5) tetraphosphate
ComponentsAnopheles gambiae adenosine kinase
KeywordsTRANSFERASE / Anopheles gambiae / adenosine kinase / AP4A / P1 / P4-di(adenosine-5) tetraphosphate
Function / homologyAdenosine kinase, small domain - #10 / Adenosine kinase, small domain / Ribokinase / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta / BIS(ADENOSINE)-5'-TETRAPHOSPHATE
Function and homology information
Biological speciesAnopheles gambiae (African malaria mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHo, M.-C. / Cassera, M.B. / Almo, S.C. / Schramm, V.L.
CitationJournal: Biochemistry / Year: 2011
Title: A High-Affinity Adenosine Kinase from Anopheles gambiae.
Authors: Cassera, M.B. / Ho, M.C. / Merino, E.F. / Burgos, E.S. / Rinaldo-Matthis, A. / Almo, S.C. / Schramm, V.L.
History
DepositionFeb 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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: Anopheles gambiae adenosine kinase
B: Anopheles gambiae adenosine kinase
C: Anopheles gambiae adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,06212
Polymers121,3733
Non-polymers2,6889
Water4,360242
1
A: Anopheles gambiae adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3544
Polymers40,4581
Non-polymers8963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Anopheles gambiae adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3544
Polymers40,4581
Non-polymers8963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Anopheles gambiae adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3544
Polymers40,4581
Non-polymers8963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.381, 76.813, 140.515
Angle α, β, γ (deg.)90.000, 92.120, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Anopheles gambiae adenosine kinase


Mass: 40457.773 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anopheles gambiae (African malaria mosquito)
Plasmid: pDEST-14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI / References: adenosine kinase
#2: Chemical ChemComp-B4P / BIS(ADENOSINE)-5'-TETRAPHOSPHATE / Ap4A


Mass: 836.387 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C20H28N10O19P4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.24 Å3/Da / Density % sol: 45.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG3350, 0.2 M MgCl2, 5% 2-propanol, 25% glycerol and 0.1 M BisTris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 2, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 72380 / Num. obs: 72642 / % possible obs: 100 % / Observed criterion σ(I): 19.5
Reflection shellResolution: 2→2.07 Å / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.871 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.248 3667 5 %RANDOM
Rwork0.198 ---
obs0.201 72642 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.79 Å2 / Biso mean: 39.99 Å2 / Biso min: 17.78 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å20 Å2-3.04 Å2
2---1.1 Å20 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7748 0 165 242 8155
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228071
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.98410959
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6765994
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.78124.386383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.77151325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2561556
X-RAY DIFFRACTIONr_chiral_restr0.1060.21209
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216136
X-RAY DIFFRACTIONr_mcbond_it0.8911.54943
X-RAY DIFFRACTIONr_mcangle_it1.62927919
X-RAY DIFFRACTIONr_scbond_it2.2833128
X-RAY DIFFRACTIONr_scangle_it3.6874.53039
LS refinement shellResolution: 1.996→2.048 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 260 -
Rwork0.292 4930 -
all-5190 -
obs--96.86 %

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