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- PDB-2zts: Crystal structure of KaiC-like protein PH0186 from hyperthermophi... -

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Basic information

Entry
Database: PDB / ID: 2zts
TitleCrystal structure of KaiC-like protein PH0186 from hyperthermophilic archaea Pyrococcus horikoshii OT3
ComponentsPutative uncharacterized protein PH0186
KeywordsATP-binding protein / KaiC like protein / ATP-binding / Nucleotide-binding
Function / homology
Function and homology information


KaiC domain / KaiC domain profile. / KaiC-like domain / KaiC / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / KaiC domain-containing protein
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.07 Å
AuthorsMing, H. / Miyazono, K. / Tanokura, M.
CitationJournal: Proteins / Year: 2009
Title: Crystal structure of KaiC-like protein PH0186 from hyperthermophilic archaea Pyrococcus horikoshii OT3
Authors: Kang, H.-J. / Kubota, K. / Ming, H. / Miyazono, K. / Tanokura, M.
History
DepositionOct 8, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein PH0186
B: Putative uncharacterized protein PH0186
C: Putative uncharacterized protein PH0186
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9909
Polymers86,6353
Non-polymers1,3556
Water1,58588
1
A: Putative uncharacterized protein PH0186
B: Putative uncharacterized protein PH0186
C: Putative uncharacterized protein PH0186
hetero molecules

A: Putative uncharacterized protein PH0186
B: Putative uncharacterized protein PH0186
C: Putative uncharacterized protein PH0186
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,98018
Polymers173,2716
Non-polymers2,70912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area20280 Å2
ΔGint-134 kcal/mol
Surface area50070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.655, 51.807, 97.468
Angle α, β, γ (deg.)90.000, 122.830, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative uncharacterized protein PH0186


Mass: 28878.449 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Production host: Escherichia coli (E. coli) / References: UniProt: O57925
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.13 Å3/Da / Density % sol: 42.15 % / Mosaicity: 0.385 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 9% ethanol, 100mM imidazole pH7.6, 200mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.97905, 0.97934
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 27, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979051
20.979341
ReflectionRedundancy: 6.8 % / Av σ(I) over netI: 26.46 / Number: 318115 / Rmerge(I) obs: 0.083 / Χ2: 1.68 / D res high: 2 Å / D res low: 50 Å / Num. obs: 46906 / % possible obs: 95.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
22.0773.410.5090.8154.2
2.072.1586.710.3850.8555.3
2.152.2595.510.3260.9016.2
2.252.3799.710.2830.9267
2.372.5210010.2251.0297.4
2.522.7110010.1661.2127.5
2.712.9910010.121.4697.5
2.993.4210010.0781.9687.5
3.424.3110010.0542.697.4
4.315099.810.053.847
ReflectionResolution: 2→50 Å / Num. obs: 46906 / % possible obs: 95.5 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.083 / Χ2: 1.679 / Net I/σ(I): 26.462
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.074.20.50935720.81573.4
2.07-2.155.30.38542310.85586.7
2.15-2.256.20.32646370.90195.5
2.25-2.3770.28348560.92699.7
2.37-2.527.40.22548721.029100
2.52-2.717.50.16649111.212100
2.71-2.997.50.1248881.469100
2.99-3.427.50.07849361.968100
3.42-4.317.40.05449462.69100
4.31-5070.0550573.8499.8

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
Phasing MADD res high: 3 Å / D res low: 20 Å / FOM : 0.53 / Reflection: 14835
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
12 wavelength10.97823.6-7.24
12 wavelength20.97791.6-10.76
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se29.3190.8160.0060.1490.789
2Se22.6580.1510.0550.3520.698
3Se35.8320.8070.0030.4690.743
4Se24.8920.7540.0480.2150.605
5Se53.2650.9060.0530.0670.705
6Se11.0570.0090.0070.1790.35
7Se46.7290.7630.3280.3930.718
8Se53.5580.8120.3350.0750.625
9Se57.3980.3350.3540.2520.605
10Se600.6360.3520.4570.576
11Se31.010.4680.3520.2060.542
12Se34.6820.050.3380.1820.443
Phasing MAD shell
Resolution (Å)FOM Reflection
3.09-3.320.332612
3.32-3.60.42452
3.6-3.960.52244
3.96-4.460.582059
4.46-5.220.621823
5.22-6.560.681582
6.56-9.910.741252
9.91-200.74811
Phasing dmFOM : 0.56 / FOM acentric: 0.56 / FOM centric: 0.56 / Reflection: 32682 / Reflection acentric: 30601 / Reflection centric: 2081
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
2.3-2.50.20.20.1560735797276
2.5-2.90.370.380.397969310486
2.9-3.30.650.650.5554845168316
3.3-4.10.850.860.7354915122369
4.1-6.60.910.920.7844154012403
6.6-19.9030.940.940.9114231192231

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.09phasing
RESOLVE2.09phasing
REFMAC5.1.24refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.07→15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 1 / SU B: 5.4 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2195 5 %RANDOM
Rwork0.197 ---
obs0.199 43605 97.63 %-
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 max: 71.78 Å2 / Biso mean: 33.96 Å2 / Biso min: 15.85 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å20 Å20.56 Å2
2---0.72 Å20 Å2
3---2.42 Å2
Refinement stepCycle: LAST / Resolution: 2.07→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5270 0 84 88 5442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0225445
X-RAY DIFFRACTIONr_bond_other_d0.0020.025193
X-RAY DIFFRACTIONr_angle_refined_deg1.872.0017338
X-RAY DIFFRACTIONr_angle_other_deg0.953312033
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.5875649
X-RAY DIFFRACTIONr_chiral_restr0.1160.2825
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025831
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021134
X-RAY DIFFRACTIONr_nbd_refined0.2140.2901
X-RAY DIFFRACTIONr_nbd_other0.2440.25694
X-RAY DIFFRACTIONr_nbtor_other0.0870.23303
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2162
X-RAY DIFFRACTIONr_metal_ion_refined0.0090.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0740.24
X-RAY DIFFRACTIONr_symmetry_vdw_other0.30.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0170.22
X-RAY DIFFRACTIONr_mcbond_it1.1111.53247
X-RAY DIFFRACTIONr_mcangle_it1.99725255
X-RAY DIFFRACTIONr_scbond_it2.97932198
X-RAY DIFFRACTIONr_scangle_it4.9414.52083
LS refinement shellResolution: 2.07→2.123 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.304 126
Rwork0.24 2507
all-2633

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