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- PDB-1x9g: PUTATIVE MAR1 RIBONUCLEASE FROM LEISHMANIA DONOVANI -

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Basic information

Entry
Database: PDB / ID: 1x9g
TitlePUTATIVE MAR1 RIBONUCLEASE FROM LEISHMANIA DONOVANI
ComponentsPUTATIVE 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 / Isochorismatase family protein
Function and homology information
Biological speciesLeishmania donovani (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.41 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
DepositionAug 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 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 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE MAR1


Theoretical massNumber of molelcules
Total (without water)22,7021
Polymers22,7021
Non-polymers00
Water00
1
A: PUTATIVE MAR1

A: PUTATIVE MAR1

A: PUTATIVE MAR1

A: PUTATIVE MAR1


Theoretical massNumber of molelcules
Total (without water)90,8064
Polymers90,8064
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation23_555-z,y,x1
Buried area7770 Å2
ΔGint-41 kcal/mol
Surface area31400 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)147.438, 147.438, 147.438
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

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Components

#1: Protein PUTATIVE MAR1


Mass: 22701.506 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Plasmid details: SGPP target construct Ldon001686AAA / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / References: UniProt: D0VWV0*PLUS

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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: 2.94 Å3/Da / Density % sol: 58.18 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 0.5 ul protein 10 mg/ml, 5% DMSO, 2.5% glycerol, 250 mM NaCl, 10mM HEPES pH 7.5 0.5 ul crystallization buffer 18% PEG 1000, 50 mM MES pH 5.6, 50 mM K3PO4, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.919791 / Wavelength: 0.9794, 0.9793, 0.8919
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 27, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9197911
20.97941
30.97931
40.89191
ReflectionResolution: 2.4→39.4 Å / Num. all: 20110 / Num. obs: 10935 / Observed criterion σ(F): 0 / Redundancy: 20.8 % / Rmerge(I) obs: 0.075
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.4-2.4720.60.9181100
2.47-2.55210.9141100
2.55-2.6421.30.6471100
2.64-2.7521.40.4551100
2.75-2.8721.50.3131100
2.87-3.0221.40.2261100
3.02-3.2121.30.1541100
3.21-3.4621.10.1021100
3.46-3.8120.90.084199.9
3.81-4.3620.30.065199.8
4.36-5.4919.40.047199.7
5.49-50190.033198.4

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 3.002 Å / D res low: 26.726 Å / FOM : 0.68 / Reflection: 5648
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
1110.97943.24-10.38
1120.97933.3-3.13
1130.89196.02-5.17
Phasing MAD shell
Resolution (Å)FOM Reflection
10.37-26.7260.7322
6.7-10.370.74491
5.28-6.70.72597
4.49-5.280.71704
3.98-4.490.69779
3.61-3.980.7849
3.32-3.610.65919
3.1-3.320.59987
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.96-10051.40.814502
5.46-6.9657.90.802505
4.74-5.4639.50.798506
4.29-4.74340.792504
3.97-4.2944.60.64508
3.72-3.9735.20.692513
3.52-3.7229.30.749507
3.37-3.5224.60.719503
3.23-3.3723.30.679505
3.12-3.2322.20.6503
3-3.1225.40.508580

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
CNS1.1refinement
SOLVE2.06phasing
DM4.2phasing
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.41→39.406 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.915 / Occupancy max: 1 / Occupancy min: 1 / SU B: 23.98 / SU ML: 0.241 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.389 / ESU R Free: 0.282 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27567 980 9.5 %RANDOM
Rwork0.22468 ---
obs0.22969 9326 94.07 %-
all-20135 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.738 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.61 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.41→39.406 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1517 0 0 0 1517
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221547
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.971.9872092
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5575191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.72724.60363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.36115292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.481158
X-RAY DIFFRACTIONr_chiral_restr0.1510.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021131
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2430.2668
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21031
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.246
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.9361.51002
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.58221573
X-RAY DIFFRACTIONr_scbond_it2.2513616
X-RAY DIFFRACTIONr_scangle_it3.4644.5519
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.406→2.468 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 67 -
Rwork0.274 598 -
obs--85.7 %
Refinement TLS params.Method: refined / Origin x: -22.7464 Å / Origin y: -53.9917 Å / Origin z: -2.3303 Å
111213212223313233
T-0.2246 Å20.0039 Å2-0.0321 Å2-0.2455 Å2-0.1641 Å2---0.0582 Å2
L1.3093 °2-0.1223 °2-0.3346 °2-0.8874 °2-0.224 °2--1.344 °2
S0.1847 Å °0.0408 Å °-0.0204 Å °-0.075 Å °-0.2934 Å °0.1901 Å °0.005 Å °-0.2356 Å °0.1086 Å °
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top

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