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- PDB-3mqw: Crystal structure of a putative endoribonuclease L-PSP from Entam... -

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Basic information

Entry
Database: PDB / ID: 3mqw
TitleCrystal structure of a putative endoribonuclease L-PSP from Entamoeba histolytica with higher solvent content and an ordered N-terminal tag
Componentsputative Endoribonuclease L-PSP
KeywordsUNKNOWN FUNCTION / putative Endoribonuclease / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


organonitrogen compound catabolic process / deaminase activity / mitochondrion / cytosol
Similarity search - Function
RidA family / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Endoribonuclease L-PSP, putative
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be published
Title: Crystal structure of a putative endoribonuclease L-PSP from Entamoeba histolytica
Authors: Gardberg, A. / Abendroth, J. / Staker, B.
History
DepositionApr 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / 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 / _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

Downloads & links

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Assembly

Deposited unit
A: putative Endoribonuclease L-PSP
B: putative Endoribonuclease L-PSP
C: putative Endoribonuclease L-PSP
D: putative Endoribonuclease L-PSP
E: putative Endoribonuclease L-PSP
F: putative Endoribonuclease L-PSP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,28124
Polymers94,1106
Non-polymers2,17118
Water13,799766
1
A: putative Endoribonuclease L-PSP
B: putative Endoribonuclease L-PSP
C: putative Endoribonuclease L-PSP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,28313
Polymers47,0553
Non-polymers1,22810
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8150 Å2
ΔGint-71 kcal/mol
Surface area16880 Å2
MethodPISA
2
D: putative Endoribonuclease L-PSP
E: putative Endoribonuclease L-PSP
F: putative Endoribonuclease L-PSP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,99811
Polymers47,0553
Non-polymers9438
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-58 kcal/mol
Surface area16990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.000, 99.720, 106.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11F
21B
31C
41D
51E
61A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116F2 - 14
2116B2 - 14
3116C2 - 14
4116D2 - 14
5116E2 - 14
6116A2 - 14
1216F18 - 83
2216B18 - 83
3216C18 - 83
4216D18 - 83
5216E18 - 83
6216A18 - 83
1316F90 - 109
2316B90 - 109
3316C90 - 109
4316D90 - 109
5316E90 - 109
6316A90 - 109
1416F117 - 155
2416B117 - 155
3416C117 - 155
4416D117 - 155
5416E117 - 155
6416A - E117 - 155

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Components

#1: Protein
putative Endoribonuclease L-PSP


Mass: 15685.029 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EHI_087570, HM-1:IMSS / Plasmid: AVA0421 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C4LXT9
#2: Chemical
ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 766 / 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: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5
Details: JCSG+ SCREEN CONDITION F2: 100MM CITRATE, 3150 MM AMMONIUM SULFATE, ENHIA.00579.A AT 26 MG/ML IN THE PRESENCE OF 2 MM SODIUM ORTHOVANADATE, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.976
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.8→19.86 Å / Num. all: 83127 / Num. obs: 81926 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 23.34 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 14.29
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2.7 / Num. unique all: 6076 / % possible all: 90.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3M4S

3m4s


Resolution: 1.8→19.86 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.429 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.183 4096 5 %RANDOM
Rwork0.147 ---
all0.148 83127 --
obs0.148 81664 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5907 0 136 766 6809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0226265
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.9958517
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6615861
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.31525.963218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.919151035
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9431514
X-RAY DIFFRACTIONr_chiral_restr0.1210.2993
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214640
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8641.54131
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.46326604
X-RAY DIFFRACTIONr_scbond_it2.77732134
X-RAY DIFFRACTIONr_scangle_it4.5514.51888
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 745 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Aloose positional0.25
Bloose positional0.185
Cloose positional0.25
Dloose positional0.25
Eloose positional0.345
Floose positional0.285
Aloose thermal1.4710
Bloose thermal1.6810
Cloose thermal1.5210
Dloose thermal1.3510
Eloose thermal1.3710
Floose thermal1.9410
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 275 -
Rwork0.225 5188 -
obs-5463 90 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.75960.0597-0.05740.47170.12770.52470.0158-0.03680.10080.013-0.00880.0468-0.0413-0.0429-0.0070.0097-0.0030.01040.0153-0.010.0262-32.1681-11.144311.0413
20.71920.1966-0.10070.773-0.08810.5152-0.01640.1077-0.007-0.0858-0.01080.00640.0411-0.05370.02720.0194-0.00890.00650.0308-0.00970.0056-22.4812-19.2797-8.8195
30.91480.2808-0.34690.4089-0.18350.4321-0.0005-0.1289-0.04750.0246-0.0421-0.02580.03440.06750.04260.01130.00590.00260.02350.00970.0063-10.4348-21.149811.6026
40.28160.0876-0.03081.179-0.30140.51080.00170.00440.0029-0.0578-0.0423-0.083-0.01510.12080.04060.008-0.00660.00820.03310.00790.01754.78987.4767-9.0469
50.8852-0.05540.05370.9706-0.09650.73760.01950.04370.0136-0.0212-0.04450.0928-0.0833-0.03160.0250.01770.0091-0.00310.0075-0.00150.0284-16.143419.6307-8.5596
61.07610.2528-0.2750.744-0.2190.65620.0681-0.16410.0270.1557-0.06850.0155-0.11070.05610.00030.0687-0.0336-0.00370.0369-0.00330.0068-2.767817.508710.8304
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-6 - 127
2X-RAY DIFFRACTION2B-12 - 127
3X-RAY DIFFRACTION3C-8 - 127
4X-RAY DIFFRACTION4D-13 - 127
5X-RAY DIFFRACTION5E-7 - 127
6X-RAY DIFFRACTION6F-7 - 127

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