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- PDB-3q2m: Crystal Structure of Spectinomycin Phosphotransferase, APH(9)-Ia,... -

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Basic information

Entry
Database: PDB / ID: 3q2m
TitleCrystal Structure of Spectinomycin Phosphotransferase, APH(9)-Ia, Protein Kinase Inhibitor CKI-7 Complex
ComponentsSpectinomycin phosphotransferase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Ser/Thr/Tyr protein kinase / phosphotransferase / phosphorylation / cytosol / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


transferase activity / nucleotide binding
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #840 / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase-like domain superfamily / Up-down Bundle ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #840 / Aminoglycoside phosphotransferase / Phosphotransferase enzyme family / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Protein kinase-like domain superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-CKI / NICKEL (II) ION / Aminoglycoside O-phosphotransferase APH(9)-Ia / Aminoglycoside O-phosphotransferase APH(9)-Ia
Similarity search - Component
Biological speciesLegionella pneumophila 130b (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBerghuis, A.M. / Fong, D.H. / Xiong, B. / Hwang, J.
CitationJournal: Plos One / Year: 2011
Title: Crystal structures of two aminoglycoside kinases bound with a eukaryotic protein kinase inhibitor.
Authors: Fong, D.H. / Xiong, B. / Hwang, J. / Berghuis, A.M.
History
DepositionDec 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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_ref_seq_dif.details / _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: Spectinomycin phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9893
Polymers39,6451
Non-polymers3442
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Spectinomycin phosphotransferase
hetero molecules

A: Spectinomycin phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9796
Polymers79,2902
Non-polymers6894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area2690 Å2
ΔGint-13 kcal/mol
Surface area31570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.300, 74.300, 137.024
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-401-

NI

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Components

#1: Protein Spectinomycin phosphotransferase


Mass: 39644.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila 130b (bacteria) / Strain: serogroup 1 strain 130b / Gene: aph, LPW_21961 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BB101 / References: UniProt: E1XXQ2, UniProt: O06916*PLUS
#2: Chemical ChemComp-CKI / N-(2-AMINOETHYL)-5-CHLOROISOQUINOLINE-8-SULFONAMIDE


Mass: 285.750 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12ClN3O2S
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.75 Å3/Da / Density % sol: 55.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG3350, 0.2M calcium acetate, manganese chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 1, 2005 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→31.32 Å / Num. all: 11271 / Num. obs: 10144 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 196 Å2 / Rsym value: 0.072 / Net I/σ(I): 18.8
Reflection shellResolution: 2.9→3 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 988 / Rsym value: 0.441 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3I1A

3i1a


Resolution: 2.9→31.32 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 70106.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1019 10.3 %RANDOM
Rwork0.221 ---
obs0.221 9913 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.268 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 63.6 Å2
Baniso -1Baniso -2Baniso -3
1--6.32 Å20 Å20 Å2
2---6.32 Å20 Å2
3---12.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.9→31.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2656 0 19 25 2700
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.632
X-RAY DIFFRACTIONc_scbond_it1.682
X-RAY DIFFRACTIONc_scangle_it2.712.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.38 159 9.8 %
Rwork0.323 1463 -
obs--96.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3ion.paramion.top

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