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- PDB-2ehw: Conserved hypothetical proteim (TTHB059) from Thermo thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 2ehw
TitleConserved hypothetical proteim (TTHB059) from Thermo thermophilus HB8
ComponentsHypothetical protein TTHB059
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / extended alpha-helix / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyHelix Hairpins - #1220 / Protein of unknown function DUF3209 / Protein of unknown function (DUF3209) / Helix Hairpins / Helix non-globular / Special / Uncharacterized protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.22 Å
AuthorsRehse, P.H. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Conserved hypothetical proteim (TTHB059) from Thermo thermophilus HB8
Authors: Rehse, P.H. / Yokoyama, S.
History
DepositionMar 9, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein TTHB059
B: Hypothetical protein TTHB059
C: Hypothetical protein TTHB059
D: Hypothetical protein TTHB059


Theoretical massNumber of molelcules
Total (without water)55,5914
Polymers55,5914
Non-polymers00
Water2,954164
1
A: Hypothetical protein TTHB059


Theoretical massNumber of molelcules
Total (without water)13,8981
Polymers13,8981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical protein TTHB059


Theoretical massNumber of molelcules
Total (without water)13,8981
Polymers13,8981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hypothetical protein TTHB059


Theoretical massNumber of molelcules
Total (without water)13,8981
Polymers13,8981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Hypothetical protein TTHB059


Theoretical massNumber of molelcules
Total (without water)13,8981
Polymers13,8981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
C: Hypothetical protein TTHB059
D: Hypothetical protein TTHB059

C: Hypothetical protein TTHB059
D: Hypothetical protein TTHB059


Theoretical massNumber of molelcules
Total (without water)55,5914
Polymers55,5914
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area12110 Å2
ΔGint-94 kcal/mol
Surface area20030 Å2
MethodPISA, PQS
6
A: Hypothetical protein TTHB059
B: Hypothetical protein TTHB059

A: Hypothetical protein TTHB059
B: Hypothetical protein TTHB059


Theoretical massNumber of molelcules
Total (without water)55,5914
Polymers55,5914
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Buried area12010 Å2
ΔGint-94 kcal/mol
Surface area20530 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)58.450, 132.460, 117.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Hypothetical protein TTHB059


Mass: 13897.704 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta834 (DE3) / References: UniProt: Q53WA3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.05 Å3/Da / Density % sol: 39.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 23% PEG MME 2000, 20mM Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97915, 0.97952, 1.0000
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 22, 2004 / Details: mirrors
RadiationMonochromator: Si (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979151
20.979521
311
Reflection

% possible obs: 99

Redundancy (%)IDAv σ(I) over netINumberRmerge(I) obsΧ2D res high (Å)D res low (Å)Num. obs
7.12114.51630350.07612.2235.2122728
7.12215.31472430.0740.962.335.2320520
7.06313.71459720.0820.952.339.5720525
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancyRejects
4.7835.2197.510.0451.066.46429
3.794.7898.710.0460.966.99255
3.323.799910.0550.947.08185
3.013.3299.410.0860.947.16114
2.83.0199.410.1250.987.2161
2.632.899.310.16117.2248
2.52.6399.210.2011.017.2937
2.392.59910.2321.027.2553
2.32.3999.110.2761.037.320
2.222.399.110.3411.067.2721
4.9535.2396.820.0530.966.4589
3.934.9598.720.0410.866.98219
3.443.9399.220.0510.937.04167
3.123.4499.420.0770.97.1692
2.93.1299.520.1140.957.2522
2.732.999.220.1440.967.244
2.592.7399.420.1910.997.263
2.482.5999.320.2130.987.286
2.382.4899.120.2541.037.311
2.32.3899.220.2911.027.332
4.9539.5797.230.0490.96.36519
3.934.9599.230.0450.836.91181
3.443.9399.330.0560.856.99125
3.123.4499.430.090.887.1107
2.93.1299.630.1340.937.1744
2.732.999.330.1750.977.1726
2.592.7399.330.2310.997.2127
2.482.5999.230.2551.047.2129
2.382.489930.30317.2611
2.32.3899.230.3391.057.2626
ReflectionResolution: 2.22→35.22 Å / Num. all: 22967 / Num. obs: 22728 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.12 % / Rmerge(I) obs: 0.076 / Χ2: 1 / Net I/σ(I): 14.5 / Scaling rejects: 1223
Reflection shellResolution: 2.22→2.3 Å / Redundancy: 7.27 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 5.5 / Num. measured all: 16348 / Num. unique all: 2246 / Χ2: 1.06 / % possible all: 99.1

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97913.34-10.02
13 wavelength20.97952.73-6.84
13 wavelength310.52-3.53
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se600.850.40.0091.157
2Se44.9690.2040.0970.0280.959
3Se600.9180.4740.2361.176
4Se56.890.5640.1710.2251.031
Phasing dmFOM : 0.58 / FOM acentric: 0.58 / FOM centric: 0.6 / Reflection: 20572 / Reflection acentric: 18458 / Reflection centric: 2114
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.6-19.7940.870.880.83917688229
4.1-6.60.880.890.8128132395418
3.3-4.10.840.850.7934503070380
2.9-3.30.650.660.634853154331
2.5-2.90.420.420.3961245641483
2.3-2.50.240.250.2237833510273

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Processing

Software
NameVersionClassificationNB
d*TREK8.0SSIdata scaling
SOLVE2.1phasing
RESOLVE2.1phasing
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
d*TREKdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.22→35.21 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1108 4.8 %random
Rwork0.22 ---
all-22967 --
obs-22726 98.7 %-
Solvent computationBsol: 34.83 Å2
Displacement parametersBiso mean: 35.955 Å2
Baniso -1Baniso -2Baniso -3
1--2.93 Å20 Å20 Å2
2--6.092 Å20 Å2
3----3.162 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.22→35.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3703 0 0 164 3867
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_d0.005691.5
X-RAY DIFFRACTIONc_angle_deg1.100632
X-RAY DIFFRACTIONc_dihedral_angle_d17.541612
X-RAY DIFFRACTIONc_improper_angle_d0.766952.5
LS refinement shellResolution: 2.22→2.3 Å
RfactorNum. reflection% reflection
Rfree0.293 112 -
Rwork0.2452 --
obs-2198 92.02 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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