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- PDB-6md3: Structure of T. brucei RRP44 PIN domain -

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Basic information

Entry
Database: PDB / ID: 6md3
TitleStructure of T. brucei RRP44 PIN domain
ComponentsRrp44p homologue
KeywordsHydrolase/RNA / rRNA processing / Ribonuclease / RRP44 / PIN domain / Hydrolase-RNA complex
Function / homology
Function and homology information


nuclear mRNA surveillance of mRNA 3'-end processing / cytoplasmic exosome (RNase complex) / nuclear exosome (RNase complex) / rRNA catabolic process / rRNA processing / 3'-5'-RNA exonuclease activity / endonuclease activity / RNA binding / metal ion binding / nucleus
Similarity search - Function
PIN domain / Rrp44-like cold shock domain / Rrp44-like cold shock domain / Dis3-like cold-shock domain 2 / Dis3-like cold-shock domain 2 (CSD2) / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / : / Ribonuclease II/R / RNB domain ...PIN domain / Rrp44-like cold shock domain / Rrp44-like cold shock domain / Dis3-like cold-shock domain 2 / Dis3-like cold-shock domain 2 (CSD2) / Ribonuclease II/R, conserved site / Ribonuclease II family signature. / : / Ribonuclease II/R / RNB domain / RNB / PIN domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
: / Ribosomal RNA-processing protein 44
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.29 Å
AuthorsGuimaraes, B.G. / Cesaro, G.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq) Brazil
CitationJournal: RNA Biol / Year: 2019
Title: Trypanosoma brucei RRP44 is involved in an early stage of large ribosomal subunit RNA maturation.
Authors: Cesaro, G. / Carneiro, F.R.G. / Avila, A.R. / Zanchin, N.I.T. / Guimaraes, B.G.
History
DepositionSep 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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_asym_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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.ptnr2_auth_asym_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rrp44p homologue
B: Rrp44p homologue
C: Rrp44p homologue
D: Rrp44p homologue
E: Rrp44p homologue
F: Rrp44p homologue
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,82941
Polymers133,9956
Non-polymers1,83435
Water11,926662
1
A: Rrp44p homologue
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6798
Polymers22,3321
Non-polymers3477
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rrp44p homologue
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6447
Polymers22,3321
Non-polymers3126
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Rrp44p homologue
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6096
Polymers22,3321
Non-polymers2765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Rrp44p homologue
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6096
Polymers22,3321
Non-polymers2765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Rrp44p homologue
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6096
Polymers22,3321
Non-polymers2765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Rrp44p homologue
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6798
Polymers22,3321
Non-polymers3477
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.570, 89.570, 321.610
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
Rrp44p homologue


Mass: 22332.418 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Gene: RRP44 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q95Z12
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: Mn
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 662 / 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: 2.78 Å3/Da / Density % sol: 50.64 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 6
Details: 20% PEG 3350, 0.2 M magnesium chloride, 0.1 M MES pH 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.2824 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2824 Å / Relative weight: 1
ReflectionResolution: 2.29→45.91 Å / Num. obs: 64571 / % possible obs: 99.7 % / Redundancy: 10.1 % / Biso Wilson estimate: 73.19 Å2 / CC1/2: 0.99 / Net I/σ(I): 13.9
Reflection shellResolution: 2.29→2.43 Å / Redundancy: 10 % / Mean I/σ(I) obs: 1 / Num. unique obs: 20379 / CC1/2: 0.42 / % possible all: 97.9

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.29→45.91 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.924 / SU R Cruickshank DPI: 0.244 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.249 / SU Rfree Blow DPI: 0.192 / SU Rfree Cruickshank DPI: 0.192
RfactorNum. reflection% reflectionSelection details
Rfree0.23 3229 5 %RANDOM
Rwork0.2 ---
obs0.202 64571 99.6 %-
Displacement parametersBiso max: 253.65 Å2 / Biso mean: 70.22 Å2 / Biso min: 36.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.3724 Å20 Å20 Å2
2--3.3724 Å20 Å2
3----6.7447 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: final / Resolution: 2.29→45.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7938 0 35 662 8635
Biso mean--112 66.48 -
Num. residues----1036
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2841SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1358HARMONIC5
X-RAY DIFFRACTIONt_it8033HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1103SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9440SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8033HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10867HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion2.66
X-RAY DIFFRACTIONt_other_torsion16.67
LS refinement shellResolution: 2.29→2.35 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3308 228 5 %
Rwork0.2717 4335 -
all0.2747 4563 -
obs--94.2 %
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)
10.89430.3413-0.34373.5302-0.63642.1690.10590.00520.19560.52590.04890.4311-0.3032-0.2091-0.1549-0.04940.02020.1226-0.0664-0.0288-0.165333.80029.710645.375
21.39830.06670.44721.42230.04381.63180.01940.1194-0.02810.04950.0167-0.00060.06210.18-0.0361-0.08230.0322-0.00360.0735-0.0318-0.172989.482847.259236.6631
32.04150.52650.28781.4993-0.32211.6066-0.0992-0.0486-0.2704-0.1019-0.0175-0.23040.10530.17670.1167-0.1055-0.00160.04110.0336-0.0087-0.141369.152224.609717.1162
43.4150.16881.29592.22670.84021.7004-0.0561-0.50860.03310.4026-0.19960.58550.2116-0.50630.2557-0.1679-0.07340.16610.0984-0.068-0.238565.631650.137851.9089
51.21711.006-1.12012.8696-1.21062.2763-0.0002-0.3755-0.19920.4027-0.3741-0.7435-0.06160.59290.3744-0.1704-0.0738-0.11490.02410.1091-0.124861.39234.793446.5096
61.28640.3426-0.4821.3230.08981.5053-0.0068-0.0740.15060.03440.02340.1899-0.0133-0.2075-0.0166-0.1353-0.0155-0.00070.0933-0.0361-0.123544.552338.339824.5954
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A28 - 219
2X-RAY DIFFRACTION2{ B|* }B27 - 219
3X-RAY DIFFRACTION3{ C|* }C24 - 219
4X-RAY DIFFRACTION4{ D|* }D29 - 220
5X-RAY DIFFRACTION5{ E|* }E29 - 221
6X-RAY DIFFRACTION6{ F|* }F27 - 221

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