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- PDB-3vrh: Crystal structure of ph0300 -

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Basic information

Entry
Database: PDB / ID: 3vrh
TitleCrystal structure of ph0300
ComponentsPutative uncharacterized protein PH0300
KeywordsRNA BINDING PROTEIN / ATPase / tRNA modification enzyme / thiolation
Function / homology
Function and homology information


Transferases; Transferring sulfur-containing groups; Sulfurtransferases / cytosolic tRNA wobble base thiouridylase complex / tRNA wobble position uridine thiolation / transferase activity / 4 iron, 4 sulfur cluster binding / tRNA binding / ATP binding / metal ion binding
Similarity search - Function
Cytoplasmic tRNA 2-thiolation protein 1 / tRNA thiolation protein, TtcA/Ctu1 type / : / 2-thiouridine synthetase TtuA, N-terminal LIM domain / tRNA(Ile)-lysidine/2-thiocytidine synthase, N-terminal / PP-loop family / Rhodanese-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold ...Cytoplasmic tRNA 2-thiolation protein 1 / tRNA thiolation protein, TtcA/Ctu1 type / : / 2-thiouridine synthetase TtuA, N-terminal LIM domain / tRNA(Ile)-lysidine/2-thiocytidine synthase, N-terminal / PP-loop family / Rhodanese-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
tRNA-5-methyluridine(54) 2-sulfurtransferase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsNakagawa, H. / Kuratani, M. / Goto-Ito, S. / Ito, T. / Sekine, S.I. / Yokoyama, S.
CitationJournal: Proteins / Year: 2013
Title: Crystallographic and mutational studies on the tRNA thiouridine synthetase TtuA.
Authors: Nakagawa, H. / Kuratani, M. / Goto-Ito, S. / Ito, T. / Katsura, K. / Terada, T. / Shirouzu, M. / Sekine, S.I. / Shigi, N. / Yokoyama, S.
History
DepositionApr 10, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 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_conn_angle / struct_conn / 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_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_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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: Putative uncharacterized protein PH0300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9864
Polymers35,6921
Non-polymers2943
Water1,44180
1
A: Putative uncharacterized protein PH0300
hetero molecules

A: Putative uncharacterized protein PH0300
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9718
Polymers71,3832
Non-polymers5886
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area3020 Å2
ΔGint-14 kcal/mol
Surface area30080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.071, 70.071, 128.636
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Putative uncharacterized protein PH0300


Mass: 35691.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT-3 / Gene: PH0300 / Production host: Escherichia coli (E. coli) / References: UniProt: O58038
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.21 Å3/Da / Density % sol: 44.39 %
Description: The entry contains Friedel pairs in F_Plus/Minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 12% PEG 3350, 0.2 M NaCl, 10% N,N-dimethylformamide, 0.1 M Bicine-NaOH, pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 70 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 1, 2010
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 19954 / Num. obs: 19923 / % possible obs: 99.9 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 25.1
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.1-2.18199.7
2.18-2.26199.9
2.26-2.371100
2.37-2.491100
2.49-2.651100
2.65-2.851100
2.85-3.141100
3.14-3.591100
3.59-4.52199.9
4.52-50199.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→46.236 Å / SU ML: 0.31 / σ(F): 1.91 / Phase error: 24.03 / Stereochemistry target values: ML
Details: The entry contains Friedel pairs in F_Plus/Minus columns
RfactorNum. reflection% reflectionSelection details
Rfree0.2443 1832 5.14 %RANDOM
Rwork0.2061 ---
all0.208 ---
obs0.208 19923 99.76 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.677 Å2 / ksol: 0.333 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.2624 Å20 Å2-0 Å2
2--8.2624 Å2-0 Å2
3----5.3799 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.236 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2411 0 13 80 2504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082474
X-RAY DIFFRACTIONf_angle_d1.0383314
X-RAY DIFFRACTIONf_dihedral_angle_d14.624955
X-RAY DIFFRACTIONf_chiral_restr0.071352
X-RAY DIFFRACTIONf_plane_restr0.005414
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1004-2.15720.36121120.2728259398
2.1572-2.22070.26891560.26752574100
2.2207-2.29240.32581650.23852573100
2.2924-2.37430.26491510.22542589100
2.3743-2.46940.23881220.20142632100
2.4694-2.58180.3381710.2222567100
2.5818-2.71790.25881440.23562602100
2.7179-2.88810.31291200.23142623100
2.8881-3.11110.31541630.22692601100
3.1111-3.42410.27461320.22092608100
3.4241-3.91930.25091310.18822617100
3.9193-4.9370.16511360.1762616100
4.937-46.24760.16381290.18292605100

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