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- PDB-1q7h: Structure of a Conserved PUA Domain Protein from Thermoplasma aci... -

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Basic information

Entry
Database: PDB / ID: 1q7h
TitleStructure of a Conserved PUA Domain Protein from Thermoplasma acidophilum
Componentsconserved hypothetical protein
KeywordsStructural genomics / unknown function / Thermoplasma acidophilum / MCSG / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


formation of translation preinitiation complex / translation initiation factor activity
Similarity search - Function
Domain of unknown function DUF1947 / Domain of unknown function (DUF1947) / Pre-PUA domain; domain 1 / Conserved hypothetical protein CHP03684 / Eukaryotic translation initiation factor 2D / MCT-1/Tma20 / Uncharacterised domain CHP00451 / PUA domain / PUA domain / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 ...Domain of unknown function DUF1947 / Domain of unknown function (DUF1947) / Pre-PUA domain; domain 1 / Conserved hypothetical protein CHP03684 / Eukaryotic translation initiation factor 2D / MCT-1/Tma20 / Uncharacterised domain CHP00451 / PUA domain / PUA domain / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / PUA domain profile. / PUA domain superfamily / PUA-like superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PUA domain-containing protein
Similarity search - Component
Biological speciesThermoplasma acidophilum DSM 1728 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsCuff, M.E. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Structure of a conserved hypothetical protein from T. acidophilum
Authors: Cuff, M.E. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionAug 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2982
Polymers17,2331
Non-polymers651
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: conserved hypothetical protein
hetero molecules

A: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5964
Polymers34,4652
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area930 Å2
ΔGint-58 kcal/mol
Surface area14200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.228, 58.158, 112.218
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-201-

ZN

21A-241-

HOH

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Components

#1: Protein conserved hypothetical protein


Mass: 17232.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum DSM 1728 (acidophilic)
Species: Thermoplasma acidophilum / Strain: DSM1728 / Gene: Ta1423 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HIB8
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: Tris, Magnesium Formate, Glycerol, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97967, 0.97951, 0.95667
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Aug 2, 2003 / Details: SBC2
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979671
20.979511
30.956671
ReflectionResolution: 2.1→50 Å / Num. all: 9524 / Num. obs: 8365 / % possible obs: 87.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 19.1 Å2 / Rsym value: 0.097 / Net I/σ(I): 17.3
Reflection shellResolution: 2.1→2.18 Å / Mean I/σ(I) obs: 2.7 / Num. unique all: 505 / Rsym value: 0.323 / % possible all: 55.7

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Processing

Software
NameClassification
HKL-2000data collection
d*TREKdata scaling
SCALEPACKdata scaling
SOLVEphasing
autoSHARPphasing
CNSrefinement
HKL-2000data reduction
d*TREKdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.1→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: CNS bulk solvent model used
RfactorNum. reflection% reflectionSelection details
Rfree0.228 438 -random
Rwork0.169 ---
obs0.171 8365 87.8 %-
all-9524 --
Displacement parametersBiso mean: 24.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1167 0 1 176 1344
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_improper_angle_d0.87
X-RAY DIFFRACTIONx_torsion_deg24.7
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.1-2.20.244280.2090.04660753.5
2.2-2.320.33480.250.04883771.4
2.32-2.460.212420.1750.033102888.6
2.46-2.650.241610.1780.031117799.7
2.65-2.920.275730.170.032117799.2
2.92-3.340.198630.1560.025115098.8
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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