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- PDB-1ze1: Conformational Change of Pseudouridine 55 Synthase upon Its Assoc... -

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Basic information

Entry
Database: PDB / ID: 1ze1
TitleConformational Change of Pseudouridine 55 Synthase upon Its Association with RNA Substrate
ComponentstRNA pseudouridine synthase B
KeywordsLYASE / RNA modification enzyme
Function / homology
Function and homology information


tRNA pseudouridine55 synthase / mRNA pseudouridine synthesis / tRNA pseudouridine synthase activity / tRNA pseudouridine synthesis / pseudouridine synthase activity / tRNA modification / RNA binding
Similarity search - Function
tRNA pseudouridine synthase II, TruB / Pseudouridine synthase / Pseudouridine synthase II, N-terminal / tRNA pseudouridylate synthase B, C-terminal / TruB family pseudouridylate synthase (N terminal domain) / tRNA pseudouridylate synthase B C-terminal domain / Pseudouridine synthase / PUA domain / PUA domain / Pseudouridine synthase, catalytic domain superfamily ...tRNA pseudouridine synthase II, TruB / Pseudouridine synthase / Pseudouridine synthase II, N-terminal / tRNA pseudouridylate synthase B, C-terminal / TruB family pseudouridylate synthase (N terminal domain) / tRNA pseudouridylate synthase B C-terminal domain / Pseudouridine synthase / PUA domain / PUA domain / Pseudouridine synthase, catalytic domain superfamily / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / PUA domain / PUA domain profile. / PUA domain superfamily / PUA-like superfamily / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
tRNA pseudouridine synthase B
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPhannachet, K. / Huang, R.H.
CitationJournal: Nucleic Acids Res. / Year: 2004
Title: Conformational change of pseudouridine 55 synthase upon its association with RNA substrate
Authors: Phannachet, K. / Huang, R.H.
History
DepositionApr 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_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.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_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_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE According to the authors the conflicts at residues 296 and 307 are likely due to an error ...SEQUENCE According to the authors the conflicts at residues 296 and 307 are likely due to an error in the database sequence.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tRNA pseudouridine synthase B
B: tRNA pseudouridine synthase B
C: tRNA pseudouridine synthase B
D: tRNA pseudouridine synthase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,3868
Polymers142,2894
Non-polymers974
Water1,946108
1
A: tRNA pseudouridine synthase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5972
Polymers35,5721
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: tRNA pseudouridine synthase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5972
Polymers35,5721
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: tRNA pseudouridine synthase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5972
Polymers35,5721
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: tRNA pseudouridine synthase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5972
Polymers35,5721
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.650, 64.170, 176.070
Angle α, β, γ (deg.)87.48, 86.44, 79.35
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
tRNA pseudouridine synthase B / tRNA pseudouridine 55 synthase / Psi55 synthase / Pseudouridylate synthase / Uracil hydrolyase


Mass: 35572.293 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: truB / Plasmid: PLM1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q9WZW0, pseudouridylate synthase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 3.48 Å3/Da / Density meas: 65.5 Mg/m3 / Density % sol: 65.5 %

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 14-BM-C11
SYNCHROTRONAPS 19-ID21
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 42482 / Num. obs: 40146 / % possible obs: 94.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Rsym value: 0.069 / Net I/σ(I): 14.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZE2

1ze2


Resolution: 2.9→50 Å / σ(F): 2 / σ(I): 2
RfactorNum. reflection
Rfree0.281 2940
Rwork0.235 -
all-36212
obs-33272
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9756 0 4 108 9868
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.27
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it

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