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- PDB-1xn4: PUTATIVE MAR1 RIBONUCLEASE FROM LEISHMANIA MAJOR -

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Basic information

Entry
Database: PDB / ID: 1xn4
TitlePUTATIVE MAR1 RIBONUCLEASE FROM LEISHMANIA MAJOR
Componentsribonuclease MAR1
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PROTEIN STRUCTURE INITIATIVE / SGPP / PSI / Structural Genomics of Pathogenic Protozoa Consortium
Function / homologyIsochorismatase-like / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Ribonuclease mar1
Function and homology information
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.8 Å
AuthorsCaruthers, J. / Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: Protein Sci. / Year: 2005
Title: Crystal structures and proposed structural/functional classification of three protozoan proteins from the isochorismatase superfamily.
Authors: Caruthers, J. / Zucker, F. / Worthey, E. / Myler, P.J. / Buckner, F. / Van Voorhuis, W. / Mehlin, C. / Boni, E. / Feist, T. / Luft, J. / Gulde, S. / Lauricella, A. / Kaluzhniy, O. / ...Authors: Caruthers, J. / Zucker, F. / Worthey, E. / Myler, P.J. / Buckner, F. / Van Voorhuis, W. / Mehlin, C. / Boni, E. / Feist, T. / Luft, J. / Gulde, S. / Lauricella, A. / Kaluzhniy, O. / Anderson, L. / Le Trong, I. / Holmes, M.A. / Earnest, T. / Soltis, M. / Hodgson, K.O. / Hol, W.G. / Merritt, E.A.
History
DepositionOct 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 24, 2012Group: Database references
Revision 1.4Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE This protein is a putative homologue of the MAR1 endoribonuclease from L tarentolae, SPTR ...SEQUENCE This protein is a putative homologue of the MAR1 endoribonuclease from L tarentolae, SPTR O77166. The closest Genbank sequence is the homologous protein from L Major, Genbank identifier LmjF12.0060.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ribonuclease MAR1


Theoretical massNumber of molelcules
Total (without water)21,6151
Polymers21,6151
Non-polymers00
Water0
1
A: ribonuclease MAR1

A: ribonuclease MAR1

A: ribonuclease MAR1

A: ribonuclease MAR1


Theoretical massNumber of molelcules
Total (without water)86,4614
Polymers86,4614
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_645-y+1,x-1,z1
crystal symmetry operation4_665y+1,-x+1,z1
Buried area8130 Å2
ΔGint-37 kcal/mol
Surface area31070 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)100.431, 100.431, 44.736
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein ribonuclease MAR1


Mass: 21615.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Plasmid details: SGPP target construct Lmaj001686AAA / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: Q4QGT7

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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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 290 K / pH: 7.2
Details: 16% PEG 8000, 0.1 M K2HPO4, 0.1M MOPS pH7.2, VAPOR DIFFUSION, SITTING DROP, temperature 290K, pH 7.20

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.8→50 Å / Num. obs: 2294 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.126
Reflection shellResolution: 3.8→3.94 Å / Redundancy: 3.5 % / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefmac_5.2.0005 24/04/2001refinement
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X9G

1x9g


Resolution: 3.8→40.86 Å / Cor.coef. Fo:Fc: 0.868 / Cor.coef. Fo:Fc free: 0.898 / TLS residual ADP flag: LIKELY RESIDUAL / ESU R Free: 0.998 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.312 101 4.412 %
Rwork0.313 --
obs-2289 99.7 %
Solvent computationSolvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 70.43 Å2
Baniso -1Baniso -2Baniso -3
1--1.378 Å20 Å20 Å2
2---1.378 Å20 Å2
3---2.756 Å2
Refinement stepCycle: LAST / Resolution: 3.8→40.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1504 0 0 0 1504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221534
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8931.9892074
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.5085190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.84424.83962
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.24215289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.422157
X-RAY DIFFRACTIONr_chiral_restr0.0540.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.021122
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1770.2691
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.21050
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0910.236
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.030.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.1451.5992
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.26321560
X-RAY DIFFRACTIONr_scbond_it0.0233602
X-RAY DIFFRACTIONr_scangle_it0.0364.5514
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.8→3.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 6 -
Rwork0.464 167 -
obs--98.3 %
Refinement TLS params.Method: refined / Origin x: 95.394 Å / Origin y: 22.306 Å / Origin z: 30.018 Å
111213212223313233
T0.648 Å20.1291 Å2-0.1044 Å2-0.543 Å20.085 Å2--0.7063 Å2
L6.5473 °2-0.582 °20.9255 °2-10.7128 °21.339 °2--5.2698 °2
S-0.0553 Å °0.0674 Å °2.2659 Å °-0.0284 Å °-0.039 Å °0.6675 Å °-0.0788 Å °-0.1242 Å °0.0943 Å °

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