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- PDB-5vbb: Human RNA Pseudouridylate Synthase Domain Containing 1 -

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Basic information

Entry
Database: PDB / ID: 5vbb
TitleHuman RNA Pseudouridylate Synthase Domain Containing 1
ComponentsRNA pseudouridylate synthase domain-containing protein 1
KeywordsRNA BINDING PROTEIN / RPUSD1 / RNA Pseudouridylate Synthase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology: / Pseudouridine synthase, RsuA/RluA-like / RNA pseudouridylate synthase / enzyme-directed rRNA pseudouridine synthesis / pseudouridine synthase activity / Pseudouridine synthase, catalytic domain superfamily / RNA binding / RNA pseudouridylate synthase domain-containing protein 1
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å
AuthorsDONG, A. / ZENG, H. / WALKER, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / BROWN, P.J. / WU, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Human RNA Pseudouridylate Synthase Domain Containing 1
Authors: ZENG, H. / DONG, A. / WALKER, J.R. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / BROWN, P.J. / WU, H. / Structural Genomics Consortium (SGC)
History
DepositionMar 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry
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: RNA pseudouridylate synthase domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7867
Polymers29,3351
Non-polymers4516
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.200, 92.440, 88.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-431-

HOH

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Components

#1: Protein RNA pseudouridylate synthase domain-containing protein 1 / Ribosomal large subunit pseudouridine synthase C-like protein


Mass: 29334.541 Da / Num. of mol.: 1 / Fragment: UNP residues 1-261
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RPUSD1, C16orf40, RLUCL / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codon plus RIL / References: UniProt: Q9UJJ7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.89 Å3/Da / Density % sol: 34.77 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 21% PEG 3350, 0.2 M LiSO4, 0.1 M BisTris pH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97914 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Feb 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 17148 / % possible obs: 99.4 % / Redundancy: 9.7 % / Biso Wilson estimate: 37.57 Å2 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.027 / Rrim(I) all: 0.087 / Χ2: 0.75 / Net I/σ(I): 5.1 / Num. measured all: 166822
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.94-1.978.30.8098210.8730.2770.8580.46696.7
1.97-2.018.70.7358120.8980.2490.7780.44697.8
2.01-2.058.70.6138410.9230.2090.6490.45899.3
2.05-2.0990.5578490.9420.1880.5890.49799.8
2.09-2.149.20.488440.9640.1620.5070.48698.9
2.14-2.188.70.4128430.9650.1440.4380.49399.6
2.18-2.24100.4048490.9740.1320.4260.48799.8
2.24-2.310.50.3588400.9840.1140.3770.507100
2.3-2.3710.50.3028760.9850.0970.3180.498100
2.37-2.4410.50.2688520.9870.0850.2810.521100
2.44-2.5310.40.2068530.9940.0660.2160.53399.8
2.53-2.6310.30.1758450.9940.0570.1840.575100
2.63-2.759.80.1468610.9950.0480.1540.5999.8
2.75-2.99.50.1178570.9950.0390.1240.67399.1
2.9-3.0810.80.0978690.9970.0310.1020.77999.9
3.08-3.3210.60.0788620.9980.0250.0820.93499.9
3.32-3.6510.30.0698660.9980.0230.0731.20399.8
3.65-4.189.30.0588810.9980.020.0621.37999
4.18-5.2610.40.0538850.9990.0170.0551.38799.9
5.26-509.30.0569420.9990.0190.0591.78198.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
HKL-3000data scaling
PDB_EXTRACT3.22data extraction
BALBESphasing
HKL-3000phasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→18.52 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.922 / Rfactor Rfree error: 0.035 / SU R Cruickshank DPI: 0.408 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.17 / SU Rfree Blow DPI: 0.151 / SU Rfree Cruickshank DPI: 0.149
RfactorNum. reflection% reflectionSelection details
Rfree0.224 804 4.71 %RANDOM
Rwork0.179 ---
obs0.181 17070 99.4 %-
Displacement parametersBiso max: 133.52 Å2 / Biso mean: 49.07 Å2 / Biso min: 9.23 Å2
Baniso -1Baniso -2Baniso -3
1-9.3119 Å20 Å20 Å2
2--5.6484 Å20 Å2
3----14.9604 Å2
Refine analyzeLuzzati coordinate error obs: 0.26 Å
Refinement stepCycle: final / Resolution: 1.94→18.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1889 0 31 97 2017
Biso mean--60.45 52.74 -
Num. residues----245
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d819SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes35HARMONIC2
X-RAY DIFFRACTIONt_gen_planes591HARMONIC5
X-RAY DIFFRACTIONt_it3843HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion252SEMIHARMONIC5
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_contact4284SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3843HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6930HARMONIC21.08
X-RAY DIFFRACTIONt_omega_torsion3.88
X-RAY DIFFRACTIONt_other_torsion14.84
LS refinement shellResolution: 1.94→2.06 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.216 111 4.16 %
Rwork0.182 2560 -
all0.183 2671 -
obs--98.06 %
Refinement TLS params.Method: refined / Origin x: 13.2359 Å / Origin y: 32.0532 Å / Origin z: 32.6128 Å
111213212223313233
T-0.1072 Å20.0263 Å2-0.0121 Å2--0.0883 Å20.0045 Å2---0.0095 Å2
L1.7542 °20.2983 °20.0183 °2-1.1383 °20.4022 °2--0.9746 °2
S-0.0282 Å °0.0577 Å °-0.0136 Å °-0.0299 Å °-0.0366 Å °0.1636 Å °-0.1235 Å °-0.0845 Å °0.0648 Å °
Refinement TLS groupSelection details: { A|* }

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