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Basic information

Entry
Database: PDB / ID: 1y63
TitleInitial crystal structural analysis of a probable kinase from Leishmania major Friedlin
ComponentsLmaj004144AAA protein
KeywordsStructural Genomics / Unknown Function / Protein Structure Initiative / PSI / SGPP / Structural Genomics of Pathogenic Protozoa Consortium
Function / homology
Function and homology information


adenylate kinase / adenylate kinase activity / nuclear lumen / rRNA primary transcript binding / cellular response to starvation / maturation of SSU-rRNA / cilium / cytoplasmic stress granule / response to oxidative stress / nucleolus ...adenylate kinase / adenylate kinase activity / nuclear lumen / rRNA primary transcript binding / cellular response to starvation / maturation of SSU-rRNA / cilium / cytoplasmic stress granule / response to oxidative stress / nucleolus / ATP hydrolysis activity / RNA binding / ATP binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Adenylate kinase isoenzyme 6 / AAA domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BROMIDE ION / : / Adenylate kinase isoenzyme 6 homolog
Similarity search - Component
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsRobien, M.A. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: To be Published
Title: Crystal structural analysis of a probable kinase from Leishmania major Friedlin
Authors: Robien, M.A. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
History
DepositionDec 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Sep 28, 2016Group: Other
Revision 1.4Feb 14, 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN MN 353 IS AN INCOMPLETELY OCCUPIED MANGANESE, HOH 1002 IS MODELED TO ACCOUNT FOR RESIDUAL ...HETEROGEN MN 353 IS AN INCOMPLETELY OCCUPIED MANGANESE, HOH 1002 IS MODELED TO ACCOUNT FOR RESIDUAL NON-MANGANESE DENSITY AT THE NEARBY SPECIAL POSITION (TWO FOLD AXIS). NA 501 is intended to be on a special position (TWO FOLD AXIS).- it is about 0.26A away from its symmetry-related mate.
Remark 999SEQUENCE the sequence is available in GeneDB (www.genedb.org) which is publicly available. The ...SEQUENCE the sequence is available in GeneDB (www.genedb.org) which is publicly available. The GeneDB identifier for this gene is LmjF30.1890. Additionally, residues 1-4 (GPGS-) are a cloning artifact; they are the remains of an N-terminal His tag. The remainder of the His tag was cleaved prior to crystallization. The Leishmanial protein consists of residues 5-184 noted in the SEQRES.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lmaj004144AAA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,57017
Polymers21,2581
Non-polymers1,31216
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.116, 107.116, 35.216
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-1002-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lmaj004144AAA protein


Mass: 21257.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Strain: Friedlin / Description: T7 system / Gene: LmjF30.1890 / Plasmid: pET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21star/DE3 / References: UniProt: Q4Q7A6

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Non-polymers , 5 types, 173 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.63 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: PEG20000, MES, MnCl2, HEPES, NaCl, Glycerol, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9198, 0.8856, 0.9202
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 6, 2004
RadiationMonochromator: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91981
20.88561
30.92021
ReflectionResolution: 1.55→38 Å / Num. all: 30440 / Num. obs: 30411 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 19.137 Å2 / Rsym value: 0.06 / Net I/σ(I): 14.5
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2 / Rsym value: 0.564 / % possible all: 94.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→38 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.091 / Stereochemistry target values: MA IMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TWO LOOPS WHICH ARE PARTIALLY DISORDERED ARE MODELED WITH OCCUPANCY ESTIMATED AT 0.75 THESE INCLUDE RESIDUES 61-63 AND 120-123. SEVERAL ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TWO LOOPS WHICH ARE PARTIALLY DISORDERED ARE MODELED WITH OCCUPANCY ESTIMATED AT 0.75 THESE INCLUDE RESIDUES 61-63 AND 120-123. SEVERAL DISORDERED SIDECHAIN ATOMS ARE MODELED WITH OCCUPANCY SET TO 0.10. PARTIALLY ORDERED SIDECHAIN ATOMS HAVE BEEN MODELED WITH OCCUPANCIES SET TO ONE-HALF OF THE CORRESPONDING MAIN CHAIN ATOMS. THE FINAL OCCUPANCIES OF THE PARTIALLY OCCUPIED HEAVY ATOMS WERE OBTAINED USING SHARP, AND ROUNDED TO THE NEAREST 0.05. THE CLOSE CONTACT BETWEEN RESIDUES GLU54 AND ILE63 IS BETWEEN SEVERELY DISORDERED SIDECHAINS IN A MINIMALLY ORDERED LOOP, AS NOTED above. THE OCCUPANCIES OF THESE SIDECHAINS HAS BEEN LOWERED TO REFLECT THE WEAK ELECTRON DENSITY IN THIS AREA OF THE MAPS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19621 1181 5.1 %RANDOM
Rwork0.16492 ---
all0.1665 21985 --
obs0.1665 21985 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.038 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1366 0 42 157 1565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211448
X-RAY DIFFRACTIONr_bond_other_d0.0010.021288
X-RAY DIFFRACTIONr_angle_refined_deg1.4671.9911964
X-RAY DIFFRACTIONr_angle_other_deg0.8333012
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9915170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.53224.93375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.77515270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1961510
X-RAY DIFFRACTIONr_chiral_restr0.0820.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021582
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02281
X-RAY DIFFRACTIONr_nbd_refined0.2260.2298
X-RAY DIFFRACTIONr_nbd_other0.1880.21282
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2704
X-RAY DIFFRACTIONr_nbtor_other0.0820.2778
X-RAY DIFFRACTIONr_metal_ion_refined0.3030.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2970.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2980.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.212
X-RAY DIFFRACTIONr_mcbond_it1.8554848
X-RAY DIFFRACTIONr_mcbond_other0.5844345
X-RAY DIFFRACTIONr_mcangle_it2.89361381
X-RAY DIFFRACTIONr_scbond_it3.3696615
X-RAY DIFFRACTIONr_scangle_it5.24910583
LS refinement shellResolution: 1.7→1.792 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.228 152 -
Rwork0.164 3166 -
obs-3318 99.94 %
Refinement TLS params.Method: refined / Origin x: 27.726 Å / Origin y: 6.062 Å / Origin z: 17.465 Å
111213212223313233
T-0.0786 Å2-0.0003 Å2-0.0086 Å2--0.0886 Å2-0.0156 Å2---0.0957 Å2
L1.6244 °2-0.4653 °20.1687 °2-1.1455 °2-0.1666 °2--1.0981 °2
S0.039 Å °-0.0188 Å °-0.0742 Å °-0.0541 Å °-0.028 Å °0.0766 Å °0.0314 Å °0.0234 Å °-0.011 Å °

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