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- PDB-5tsq: Crystal structure of IUnH from Leishmania braziliensis in complex... -

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Basic information

Entry
Database: PDB / ID: 5tsq
TitleCrystal structure of IUnH from Leishmania braziliensis in complex with D-Ribose
ComponentsIUnH
KeywordsHYDROLASE / IUnH / Leishmania braziliensis / D-Ribose
Function / homology
Function and homology information


hydrolase activity, hydrolyzing N-glycosyl compounds / metabolic process / metal ion binding
Similarity search - Function
Inosine/uridine-preferring nucleoside hydrolase, conserved site / Inosine-uridine preferring nucleoside hydrolase family signature. / Inosine-uridine Nucleoside N-ribohydrolase; Chain A / Ribonucleoside hydrolase-like / Inosine/uridine-preferring nucleoside hydrolase / Inosine/uridine-preferring nucleoside hydrolase domain / Inosine-uridine preferring nucleoside hydrolase / Ribonucleoside hydrolase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
beta-D-ribofuranose / Nonspecific nucleoside hydrolasewith=GeneDB:LmjF18.1580
Similarity search - Component
Biological speciesLeishmania braziliensis braziliensis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.53 Å
AuthorsBachega, J.F.R. / Timmers, L.F.S.M. / Dalberto, P.F. / Martinelli, L. / Pinto, A.F.M. / Basso, L.A. / Norberto de Souza, O. / Santos, D.S.
CitationJournal: To Be Published
Title: Crystal structure of IUnH from Leishmania braziliensis in complex with D-Ribose
Authors: Bachega, J.F.R. / Timmers, L.F.S.M. / Dalberto, P.F. / Martinelli, L. / Pinto, A.F.M. / Basso, L.A. / Norberto de Souza, O. / Santos, D.S.
History
DepositionOct 31, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Structure summary
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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.value / _struct_conn.pdbx_dist_value / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IUnH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4393
Polymers34,2491
Non-polymers1902
Water5,008278
1
A: IUnH
hetero molecules

A: IUnH
hetero molecules

A: IUnH
hetero molecules

A: IUnH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,75512
Polymers136,9944
Non-polymers7618
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area9650 Å2
ΔGint-108 kcal/mol
Surface area44160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.660, 94.080, 123.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-507-

HOH

21A-564-

HOH

31A-702-

HOH

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Components

#1: Protein IUnH


Mass: 34248.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania braziliensis braziliensis (eukaryote)
Gene: LBRM_18_1610 / Production host: Escherichia coli (E. coli) / References: UniProt: A4H9Q9, purine nucleosidase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-BDR / beta-D-ribofuranose / beta-D-ribose / D-ribose / ribose / BETA-D-RIBOFURANOSYL / Ribose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DRibfbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-ribofuranoseCOMMON NAMEGMML 1.0
b-D-RibfIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 3.16 Å3/Da / Density % sol: 61.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Ammonium acetate, 0.1M HEPES pH 7.5 and 45% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
ReflectionResolution: 1.53→74.754 Å / Num. obs: 64501 / % possible obs: 98.5 % / Redundancy: 4.3 % / Rsym value: 0.091 / Net I/av σ(I): 4.421 / Net I/σ(I): 6.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.53-1.612.30.4310.7190.8
1.61-1.713.20.3051199.3
1.71-1.833.70.2291.4199.7
1.83-1.984.60.14931100
1.98-2.165.10.1642.9199.9
2.16-2.425.20.1443.61100
2.42-2.795.20.1294.41100
2.79-3.425.30.0986.31100
3.42-4.845.50.04710.91100

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.547
Highest resolutionLowest resolution
Rotation21.66 Å1.68 Å

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
MOLREP11.2.08phasing
PHENIX1.11rc2_2531refinement
PDB_EXTRACT3.2data extraction
MOSFLM7.1.1data reduction
MOLREP11.2.08phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EZR

1ezr


Resolution: 1.53→21.655 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.52
RfactorNum. reflection% reflection
Rfree0.1685 3226 5.03 %
Rwork0.1534 --
obs0.1542 64118 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.82 Å2 / Biso mean: 24.5624 Å2 / Biso min: 8.2 Å2
Refinement stepCycle: final / Resolution: 1.53→21.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2398 0 11 278 2687
Biso mean--19.36 38.51 -
Num. residues----312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112490
X-RAY DIFFRACTIONf_angle_d0.9723395
X-RAY DIFFRACTIONf_chiral_restr0.062414
X-RAY DIFFRACTIONf_plane_restr0.007434
X-RAY DIFFRACTIONf_dihedral_angle_d4.712085
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.55280.2881140.27192144X-RAY DIFFRACTION80
1.5528-1.57710.26351160.26032339X-RAY DIFFRACTION87
1.5771-1.60290.25021320.2382602X-RAY DIFFRACTION96
1.6029-1.63060.22051590.21482580X-RAY DIFFRACTION97
1.6306-1.66020.22011440.20192628X-RAY DIFFRACTION98
1.6602-1.69210.18421270.18652621X-RAY DIFFRACTION98
1.6921-1.72670.22431450.18972605X-RAY DIFFRACTION97
1.7267-1.76420.18531520.17452610X-RAY DIFFRACTION97
1.7642-1.80520.15181400.15692644X-RAY DIFFRACTION100
1.8052-1.85030.21591140.15062720X-RAY DIFFRACTION100
1.8503-1.90030.1531410.15052679X-RAY DIFFRACTION100
1.9003-1.95620.19481400.15642715X-RAY DIFFRACTION100
1.9562-2.01930.13951280.14212673X-RAY DIFFRACTION100
2.0193-2.09140.14911400.14792718X-RAY DIFFRACTION100
2.0914-2.17510.16881400.14432679X-RAY DIFFRACTION100
2.1751-2.2740.17061570.14392693X-RAY DIFFRACTION100
2.274-2.39370.16081510.14582705X-RAY DIFFRACTION100
2.3937-2.54350.19381410.15272700X-RAY DIFFRACTION100
2.5435-2.73950.18921550.14782703X-RAY DIFFRACTION100
2.7395-3.01450.14061450.13952728X-RAY DIFFRACTION100
3.0145-3.44920.13331660.13822738X-RAY DIFFRACTION100
3.4492-4.33990.13961540.12622755X-RAY DIFFRACTION100
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)
10.773-0.12010.4742.1816-0.46152.13670.0201-0.1124-0.16020.16270.0159-0.11120.34160.1336-0.00850.220.0368-0.04450.14580.0260.12539.265818.590919.3089
21.4407-0.39740.33651.8613-0.22581.75650.0559-0.0197-0.15570.0482-0.0397-0.2510.36740.2391-0.02950.20760.048-0.03830.1440.01370.13598.499418.709812.3121
30.6815-0.22570.11411.1849-0.18831.3419-0.0232-0.1096-0.04830.12470.0379-0.03840.0818-0.0275-0.03560.12650.0005-0.01750.12250.01960.07321.952129.556317.9416
42.1179-0.83680.07442.9305-0.29021.5824-0.0055-0.11010.27620.1534-0.0468-0.4982-0.12260.42350.33320.29340.0472-0.14690.35280.03030.255520.384729.045627.0063
50.7969-0.23860.2751.8172-0.70361.4688-0.0156-0.231-0.0530.29040.08520.05470.023-0.1049-0.03410.18480.003-0.00010.1730.01270.0755-0.413832.706824.62
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 56 )A2 - 56
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 129 )A57 - 129
3X-RAY DIFFRACTION3chain 'A' and (resid 130 through 212 )A130 - 212
4X-RAY DIFFRACTION4chain 'A' and (resid 213 through 233 )A213 - 233
5X-RAY DIFFRACTION5chain 'A' and (resid 234 through 313 )A234 - 313

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