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- PDB-1xpi: Crystal structure of the catalytic domain of E. coli pseudouridin... -

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Basic information

Entry
Database: PDB / ID: 1xpi
TitleCrystal structure of the catalytic domain of E. coli pseudouridine synthase RluC
ComponentsRibosomal large subunit pseudouridine synthase C
KeywordsLYASE / PSEUDOURIDINE SYNTHASE / RLUC / CATALYTIC DOMAIN
Function / homology
Function and homology information


23S rRNA pseudouridine955/2504/2580 synthase / rRNA pseudouridine synthase activity / enzyme-directed rRNA pseudouridine synthesis / pseudouridine synthase activity / RNA binding / cytosol
Similarity search - Function
Pseudouridine synthase, RluC/RluD / Pseudouridine synthase, RluA-like, conserved site / Rlu family of pseudouridine synthase signature. / Pseudouridine synthase, RsuA/RluA-like / RNA pseudouridylate synthase / Pseudouridine synthase / Pseudouridine synthase / Pseudouridine synthase, catalytic domain superfamily / S4 RNA-binding domain / RNA-binding S4 domain ...Pseudouridine synthase, RluC/RluD / Pseudouridine synthase, RluA-like, conserved site / Rlu family of pseudouridine synthase signature. / Pseudouridine synthase, RsuA/RluA-like / RNA pseudouridylate synthase / Pseudouridine synthase / Pseudouridine synthase / Pseudouridine synthase, catalytic domain superfamily / S4 RNA-binding domain / RNA-binding S4 domain / RNA-binding S4 domain superfamily / S4 domain / S4 RNA-binding domain profile. / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Ribosomal large subunit pseudouridine synthase C
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDel Campo, M. / Ofengand, J. / Fenna, R. / Malhotra, A.
CitationJournal: To be Published
Title: Possible RNA binding domains of RluC and RluD
Authors: Del Campo, M. / Ofengand, J. / Fenna, R. / Malhotra, A.
History
DepositionOct 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Ribosomal large subunit pseudouridine synthase C
B: Ribosomal large subunit pseudouridine synthase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3227
Polymers52,0222
Non-polymers3005
Water3,027168
1
A: Ribosomal large subunit pseudouridine synthase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1914
Polymers26,0111
Non-polymers1803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ribosomal large subunit pseudouridine synthase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1313
Polymers26,0111
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Ribosomal large subunit pseudouridine synthase C
B: Ribosomal large subunit pseudouridine synthase C
hetero molecules

A: Ribosomal large subunit pseudouridine synthase C
B: Ribosomal large subunit pseudouridine synthase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,64414
Polymers104,0434
Non-polymers60110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area9500 Å2
ΔGint-52 kcal/mol
Surface area38590 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)97.307, 97.307, 86.237
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a monomer from the two molecules in the asymmetric unit.

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Components

#1: Protein Ribosomal large subunit pseudouridine synthase C / / Pseudouridylate synthase / Uracil hydrolyase


Mass: 26010.869 Da / Num. of mol.: 2 / Fragment: sequence database residues 89-319
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: rluC / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P0AA39, pseudouridylate synthase
#2: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.26 Å3/Da / Density % sol: 45.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Bicine, sodium acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 10, 1998 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 24381 / Num. obs: 24381 / % possible obs: 100 % / Redundancy: 14 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 38.4
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 6.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V9K (molecule A)

1v9k


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.735 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25372 1242 5.1 %RANDOM
Rwork0.18462 ---
obs0.18805 23094 99.94 %-
all-24336 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.656 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3608 0 20 168 3796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0213685
X-RAY DIFFRACTIONr_angle_refined_deg1.9061.9674956
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3765455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.19422.229175
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22215662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9381544
X-RAY DIFFRACTIONr_chiral_restr0.1270.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022784
X-RAY DIFFRACTIONr_nbd_refined0.2090.21532
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22444
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2243
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.297
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3110.28
X-RAY DIFFRACTIONr_mcbond_it1.3111.52374
X-RAY DIFFRACTIONr_mcangle_it2.06123626
X-RAY DIFFRACTIONr_scbond_it3.17631470
X-RAY DIFFRACTIONr_scangle_it4.8884.51330
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 78 -
Rwork0.189 1696 -
obs--100 %

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