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- PDB-1x25: Crystal Structure of a Member of YjgF Family from Sulfolobus Toko... -

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Basic information

Entry
Database: PDB / ID: 1x25
TitleCrystal Structure of a Member of YjgF Family from Sulfolobus Tokodaii (ST0811)
ComponentsHypothetical UPF0076 protein ST0811
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / YJGF-LIKE PROTEIN / ARCHAEA / ST0811
Function / homology
Function and homology information


RidA, conserved site / Uncharacterized protein family UPF0076 signature. / RidA family / YjgF/YER057c/UK114 family / Endoribonuclease L-PSP / RutC-like / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RutC family protein STK_08110
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMiyakawa, T. / Lee, W.C. / Hatano, K. / Kato, Y. / Sawano, Y. / Miyazono, K. / Nagata, K. / Tanokura, M.
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of the YjgF/YER057c/UK114 family protein from the hyperthermophilic archaeon Sulfolobus tokodaii strain 7
Authors: Miyakawa, T. / Lee, W.C. / Hatano, K. / Kato, Y. / Sawano, Y. / Miyazono, K. / Nagata, K. / Tanokura, M.
History
DepositionApr 20, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical UPF0076 protein ST0811
B: Hypothetical UPF0076 protein ST0811


Theoretical massNumber of molelcules
Total (without water)28,3112
Polymers28,3112
Non-polymers00
Water3,783210
1
A: Hypothetical UPF0076 protein ST0811

A: Hypothetical UPF0076 protein ST0811

A: Hypothetical UPF0076 protein ST0811


Theoretical massNumber of molelcules
Total (without water)42,4663
Polymers42,4663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area6040 Å2
ΔGint-41 kcal/mol
Surface area15100 Å2
MethodPISA, PQS
2
B: Hypothetical UPF0076 protein ST0811


Theoretical massNumber of molelcules
Total (without water)14,1551
Polymers14,1551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Hypothetical UPF0076 protein ST0811

B: Hypothetical UPF0076 protein ST0811

B: Hypothetical UPF0076 protein ST0811


Theoretical massNumber of molelcules
Total (without water)42,4663
Polymers42,4663
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
MethodPQS
Unit cell
Length a, b, c (Å)54.980, 54.980, 221.557
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-168-

HOH

21B-221-

HOH

31B-222-

HOH

DetailsThe biological assembly is a trimer generated from a molecule in the asymmetric unit by the operations: -y, x-y, z and -x+y, -x, z.

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Components

#1: Protein Hypothetical UPF0076 protein ST0811 / YJGF-LIKE PROTEIN


Mass: 14155.356 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: str. 7 / Gene: ST0811 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q973T6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.33 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: PEG 10000, Bis-Tris, ammonium acetate, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Sep 1, 2004
RadiationMonochromator: CONFOCAL MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→22.051 Å / Num. all: 16882 / Num. obs: 16882 / % possible obs: 99.8 % / Observed criterion σ(I): 5.1 / Redundancy: 6.2 % / Biso Wilson estimate: 17.336 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.055 / Net I/σ(I): 9.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.151 / Mean I/σ(I) obs: 5.1 / Num. unique all: 182 / Rsym value: 0.137 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
CrystalClear(MSC/RIGAKU)data reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QD9

1qd9


Resolution: 2→19.03 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.786 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18799 852 5 %RANDOM
Rwork0.14578 ---
all0.14787 16877 --
obs0.14787 16877 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20.14 Å20 Å2
2--0.27 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 2→19.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1979 0 0 210 2189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222017
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.9662729
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3435252
X-RAY DIFFRACTIONr_chiral_restr0.1140.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021490
X-RAY DIFFRACTIONr_nbd_refined0.2150.2916
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2164
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.2103
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.227
X-RAY DIFFRACTIONr_mcbond_it1.0051.51273
X-RAY DIFFRACTIONr_mcangle_it1.7922081
X-RAY DIFFRACTIONr_scbond_it3.0283744
X-RAY DIFFRACTIONr_scangle_it4.9874.5648
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.193 62
Rwork0.118 1168
obs-1230

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