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- PDB-2qsb: Crystal structure of a protein from uncharacterized family UPF014... -

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Basic information

Entry
Database: PDB / ID: 2qsb
TitleCrystal structure of a protein from uncharacterized family UPF0147 from Thermoplasma acidophilum
ComponentsUPF0147 protein Ta0600
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / four-helix bundle / Thermoplasma acidophilum / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyUncharacterised protein family UPF0147 / Uncharacterised protein family (UPF0147) / Ta0600-like / Ta0600-like superfamily / de novo design (two linked rop proteins) / Up-down Bundle / Mainly Alpha / UPF0147 protein Ta0600
Function and homology information
Biological speciesThermoplasma acidophilum DSM 1728 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.3 Å
AuthorsCuff, M.E. / Duggan, E. / Gu, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Structure of a protein from uncharacterized family UPF0147 from Thermoplasma acidophilum.
Authors: Cuff, M.E. / Duggan, E. / Gu, M. / Joachimiak, A.
History
DepositionJul 30, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Remark 300 BIOMOLECULE: 1 SEE REMARK 350 FOR THE PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS POLYPEPTIDE IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0147 protein Ta0600
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2602
Polymers10,1641
Non-polymers961
Water2,306128
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.584, 50.584, 59.283
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein UPF0147 protein Ta0600


Mass: 10163.872 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: DSM 1728, IFO 15155, JCM 9062, AMRC-C165 / Gene: CAC11739, Ta0600 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HKJ8
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.15 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2M Ammonium sulfate, 0.1M Tri-HCl pH 7.0, 0.2M Lithium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931, 0.97949
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2006
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979311
20.979491
ReflectionResolution: 1.25→50 Å / Num. all: 23474 / Num. obs: 23474 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Biso Wilson estimate: 11.8 Å2 / Rmerge(I) obs: 0.099 / Χ2: 3.714 / Net I/σ(I): 9.4
Reflection shellResolution: 1.25→1.35 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1515 / Χ2: 0.908 / % possible all: 97.3

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 1.3 Å / D res low: 43.81 Å / FOM : 0.602 / FOM acentric: 0.608 / FOM centric: 0.398 / Reflection: 21124 / Reflection acentric: 20467 / Reflection centric: 657
Phasing MAD set

Highest resolution: 1.3 Å / Lowest resolution: 43.81 Å

IDR cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
11.610.30.20020467657
20.750.72.94.81.280.9420367627
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricLoc acentricLoc centricPower acentricPower centricReflection acentricReflection centric
18.61-43.811.6511.10.400508
14.77-8.611.8610.90.40033536
13.3-4.771.110.70.50081951
12.53-3.31.2310.50.300152971
12.04-2.531.4410.40.200248598
11.72-2.041.8510.30.2003643118
11.48-1.721.9310.20.1005017136
11.3-1.482.0210.20.1006589139
28.61-43.810.550.45.24.43.062.4508
24.77-8.610.420.363.74.63.642.5233536
23.3-4.770.520.583.86.42.821.581951
22.53-3.30.560.543.24.92.451.56152971
22.04-2.530.630.6634.41.831.09248596
21.72-2.040.730.82.74.71.380.643642117
21.48-1.720.870.972.74.60.920.485014136
21.3-1.480.970.992.94.60.540.36493112
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se13.81665-0.861-0.213-0.150
2Se10.97325-0.691-0.3750.0090
3Se34.74163-0.923-0.398-0.0560
4Se13.12774-0.861-0.213-0.15-0.181
5Se10.66146-0.691-0.3740.009-0.103
6Se36.44563-0.922-0.398-0.056-0.094
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.61-43.810.830.830.83258508
4.77-8.610.890.9010.78537133536
3.3-4.770.840.850.69187081951
2.53-3.30.8410.8470.7191600152971
2.04-2.530.7930.8040.5142583248598
1.72-2.040.7250.7350.40337613643118
1.48-1.720.5810.590.23151535017136
1.3-1.480.3690.3750.0867286589139
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 23416
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
4.53-10035.50.936501
3.59-4.53320.949507
3.13-3.5932.40.947508
2.84-3.1334.50.943524
2.62-2.8433.20.939566
2.45-2.6233.10.94595
2.3-2.45350.942636
2.18-2.3370.941688
2.07-2.1837.40.941726
1.98-2.07400.936749
1.9-1.9838.90.925779
1.83-1.939.50.922823
1.77-1.8341.60.912833
1.71-1.7743.50.907892
1.66-1.7143.90.894898
1.61-1.6647.80.895926
1.57-1.6147.20.896956
1.53-1.5753.90.875975
1.49-1.5354.70.8631005
1.46-1.49550.8661044
1.42-1.4658.30.8471051
1.39-1.4262.30.8251049
1.36-1.39600.8481121
1.34-1.3668.60.8361127
1.31-1.3469.50.831107
1.29-1.3178.50.8341105
1.25-1.2991.60.5871725

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM5phasing
REFMACrefinement
PDB_EXTRACT3data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.3→24.55 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.346 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.053
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.178 1079 5.1 %RANDOM
Rwork0.147 ---
all0.149 21124 --
obs0.149 21124 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.124 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: 1.3→24.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms875 0 5 128 1008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022902
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.9861244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0015125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.48325.74547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.33415178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.862158
X-RAY DIFFRACTIONr_chiral_restr0.0970.2138
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02729
X-RAY DIFFRACTIONr_nbd_refined0.2990.2488
X-RAY DIFFRACTIONr_nbtor_refined0.2990.2661
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2127
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3010.231
X-RAY DIFFRACTIONr_mcbond_it1.3591.5582
X-RAY DIFFRACTIONr_mcangle_it2.052941
X-RAY DIFFRACTIONr_scbond_it3.0083345
X-RAY DIFFRACTIONr_scangle_it4.1474.5303
X-RAY DIFFRACTIONr_rigid_bond_restr1.5213927
X-RAY DIFFRACTIONr_sphericity_free5.7523128
X-RAY DIFFRACTIONr_sphericity_bonded4.1283880
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 77 -
Rwork0.178 1438 -
all-1515 -
obs-1515 97.3 %

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