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- PDB-6cqc: RNase P protein from Thermotoga maritima in complex with 1-(4-Flu... -

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Basic information

Entry
Database: PDB / ID: 6cqc
TitleRNase P protein from Thermotoga maritima in complex with 1-(4-Fluorophenyl)-2-thiourea
ComponentsRibonuclease P protein component
KeywordsRNA BINDING PROTEIN
Function / homology
Function and homology information


ribonuclease P complex / 3'-tRNA processing endoribonuclease activity / tRNA 3'-end processing / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / tRNA binding
Similarity search - Function
Ribonuclease P / Ribonuclease P, conserved site / Ribonuclease P / Bacterial ribonuclease P protein component signature. / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1-(4-fluorophenyl)thiourea / Ribonuclease P protein component
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsTorres-Larios, A. / Madrigal-Carrillo, E.A.
Funding support Mexico, 1items
OrganizationGrant numberCountry
Consejo Nacional de Ciencia y Tecnologia (CONACYT)PDCPN2014- 47543 Mexico
CitationJournal: To Be Published
Title: Discovery of novel RNase P inhibitors via an activity-binding-structure pipeline
Authors: Madrigal-Carrillo, E.A. / Diaz-Tufinio, C.A. / Santamaria-Suarez, H.A. / Arciniega-Castro, M. / Torres-Larios, A.
History
DepositionMar 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease P protein component
B: Ribonuclease P protein component
C: Ribonuclease P protein component
D: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,06320
Polymers57,4524
Non-polymers1,61116
Water8,755486
1
A: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7475
Polymers14,3631
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7475
Polymers14,3631
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7475
Polymers14,3631
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8215
Polymers14,3631
Non-polymers4584
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.136, 64.264, 68.121
Angle α, β, γ (deg.)90.00, 101.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Ribonuclease P protein component / RNaseP protein / Protein C5


Mass: 14363.003 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: rnpA, TM_1463 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1H4, ribonuclease P
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: SO4
#3: Chemical ChemComp-8P4 / 1-(4-fluorophenyl)thiourea


Mass: 170.207 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7FN2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.09 Å3/Da / Density % sol: 41.21 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: P protein from T. maritima in 50 mM Tris-HCl pH 7.5, 0.2 mM EDTA was crystallized at 3 mg/mL in 12% PEG-1000, 100 mm sodium acetate pH 4.8 and 200 mM potassium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9785 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 12, 2011 / Details: mirrors
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.54→46.29 Å / Num. obs: 67977 / % possible obs: 96.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 18 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.029 / Rrim(I) all: 0.053 / Χ2: 0.71 / Net I/σ(I): 19.5
Reflection shellResolution: 1.54→1.57 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2724 / CC1/2: 0.915 / Rpim(I) all: 0.195 / Rrim(I) all: 0.287 / Χ2: 0.58 / % possible all: 78.5

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NZ0

1nz0


Resolution: 1.54→46.286 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 19.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.199 3437 5.06 %
Rwork0.1802 --
obs0.1811 67950 96.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.54→46.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3630 0 86 488 4204
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073869
X-RAY DIFFRACTIONf_angle_d0.7035183
X-RAY DIFFRACTIONf_dihedral_angle_d9.2542362
X-RAY DIFFRACTIONf_chiral_restr0.05546
X-RAY DIFFRACTIONf_plane_restr0.004636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.56110.2689990.24262083X-RAY DIFFRACTION77
1.5611-1.58340.2921340.22342358X-RAY DIFFRACTION90
1.5834-1.60710.22581460.22052566X-RAY DIFFRACTION96
1.6071-1.63220.2381470.20822500X-RAY DIFFRACTION97
1.6322-1.65890.22421330.21192596X-RAY DIFFRACTION97
1.6589-1.68750.25281180.20572572X-RAY DIFFRACTION97
1.6875-1.71820.23611220.19912577X-RAY DIFFRACTION97
1.7182-1.75130.23671310.19762632X-RAY DIFFRACTION97
1.7513-1.7870.20761350.20182552X-RAY DIFFRACTION97
1.787-1.82590.21171520.20642572X-RAY DIFFRACTION97
1.8259-1.86840.22921450.19822578X-RAY DIFFRACTION97
1.8684-1.91510.21781420.19262574X-RAY DIFFRACTION98
1.9151-1.96690.22991570.1862596X-RAY DIFFRACTION98
1.9669-2.02470.21631230.17882614X-RAY DIFFRACTION98
2.0247-2.09010.22021420.1762619X-RAY DIFFRACTION98
2.0901-2.16480.17011290.16782620X-RAY DIFFRACTION98
2.1648-2.25150.17141490.16622620X-RAY DIFFRACTION98
2.2515-2.35390.16181330.1652630X-RAY DIFFRACTION99
2.3539-2.4780.18951550.15962614X-RAY DIFFRACTION98
2.478-2.63330.17011440.17172626X-RAY DIFFRACTION99
2.6333-2.83660.20221350.17512690X-RAY DIFFRACTION99
2.8366-3.1220.2171500.17662632X-RAY DIFFRACTION99
3.122-3.57360.20731490.17362663X-RAY DIFFRACTION99
3.5736-4.50170.17451290.15522686X-RAY DIFFRACTION99
4.5017-46.30710.1851380.20362743X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 6.7409 Å / Origin y: 13.3899 Å / Origin z: 16.142 Å
111213212223313233
T0.1107 Å20.0115 Å20.0006 Å2-0.0967 Å2-0.0007 Å2--0.0991 Å2
L0.3973 °20.319 °20.2077 °2-0.3367 °20.2388 °2--0.2372 °2
S0.0047 Å °-0.0701 Å °0.0499 Å °0.0131 Å °-0.0314 Å °0.0681 Å °-0.0086 Å °-0.0031 Å °-0.0093 Å °
Refinement TLS groupSelection details: all

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