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- PDB-2j1q: Crystal structure of Trypanosoma cruzi arginine kinase -

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Basic information

Entry
Database: PDB / ID: 2j1q
TitleCrystal structure of Trypanosoma cruzi arginine kinase
ComponentsARGININE KINASE
KeywordsTRANSFERASE / KINASE / ARGININE KINASE / GUANIDINO KINASE / PHOSPHAGEN KINASE / TRYPANOSOMA CRUZI
Function / homology
Function and homology information


arginine kinase / arginine kinase activity / phosphocreatine biosynthetic process / creatine kinase activity / ATP binding
Similarity search - Function
Transferase Creatine Kinase; Chain A, domain 1 / ATP:guanido phosphotransferase, N-terminal domain / ATP:guanido phosphotransferase, N-terminal / ATP:guanido phosphotransferase, N-terminal domain superfamily / ATP:guanido phosphotransferase, N-terminal domain / Phosphagen kinase N-terminal domain profile. / ATP:guanido phosphotransferase active site / Phosphagen kinase active site signature. / ATP:guanido phosphotransferase / ATP:guanido phosphotransferase, catalytic domain ...Transferase Creatine Kinase; Chain A, domain 1 / ATP:guanido phosphotransferase, N-terminal domain / ATP:guanido phosphotransferase, N-terminal / ATP:guanido phosphotransferase, N-terminal domain superfamily / ATP:guanido phosphotransferase, N-terminal domain / Phosphagen kinase N-terminal domain profile. / ATP:guanido phosphotransferase active site / Phosphagen kinase active site signature. / ATP:guanido phosphotransferase / ATP:guanido phosphotransferase, catalytic domain / ATP:guanido phosphotransferase, C-terminal catalytic domain / Phosphagen kinase C-terminal domain profile. / Glutamine synthetase/guanido kinase, catalytic domain / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase/guanido kinase, catalytic domain / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesTRYPANOSOMA CRUZI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFernandez, P. / Haouz, A. / Pereira, C.A. / Aguilar, C. / Alzari, P.M.
CitationJournal: Proteins / Year: 2007
Title: The Crystal Structure of Trypanosoma Cruzi Arginine Kinase.
Authors: Fernandez, P. / Haouz, A. / Pereira, C.A. / Aguilar, C. / Alzari, P.M.
History
DepositionAug 15, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ARGININE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2552
Polymers40,1631
Non-polymers921
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)86.697, 86.697, 138.823
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein ARGININE KINASE / / AK


Mass: 40162.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA CRUZI (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O96507, arginine kinase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTWO RESIDUES HAVE BEEN MODIFIED BASED ON THE ELECTRON DENSITY MAP, LEU82 AND SER104. IN THE GENBANK ...TWO RESIDUES HAVE BEEN MODIFIED BASED ON THE ELECTRON DENSITY MAP, LEU82 AND SER104. IN THE GENBANK SEQUENCE, BOTH POSITIONS APPEAR AS PHE.

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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: 3.7 Å3/Da / Density % sol: 67 %
Crystal growpH: 7.5 / Details: 2.5 M AMMONIUM SULFATE, 0.1 M TRIS HCL, PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 7, 2005
RadiationMonochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 1.9→70 Å / Num. obs: 44532 / % possible obs: 92 % / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.7 / % possible all: 67.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M80

1m80
PDB Unreleased entry


Resolution: 1.9→75.16 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.471 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THREE REGIONS ARE DISORDERED AND ARE NOT MODEL, INCLUDING POSITIONS 289-293, 310-320 AND 356-357.
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2235 5 %RANDOM
Rwork0.194 ---
obs0.196 42208 92.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.24 Å20 Å2
2--0.48 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 1.9→75.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2667 0 6 166 2839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222720
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.9763657
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2085336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1324.672122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66115504
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.5981514
X-RAY DIFFRACTIONr_chiral_restr0.1030.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022017
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.21299
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21865
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2167
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2140.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9831.51730
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5722691
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.89531116
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5074.5966
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.31 99
Rwork0.285 2188
Refinement TLS params.Method: refined / Origin x: 54.462 Å / Origin y: 26.264 Å / Origin z: 65.135 Å
111213212223313233
T0.024 Å2-0.0198 Å20.0026 Å2--0.1012 Å20.0357 Å2---0.2376 Å2
L2.2341 °20.716 °2-1.0702 °2-0.4455 °2-0.5914 °2--2.3415 °2
S0.0792 Å °-0.0877 Å °0.084 Å °0.1483 Å °0.0316 Å °0.0539 Å °-0.1745 Å °-0.0832 Å °-0.1109 Å °

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