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- PDB-8zn6: Crystal Structure of Designed Clock Protein KaiC -

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Basic information

Entry
Database: PDB / ID: 8zn6
TitleCrystal Structure of Designed Clock Protein KaiC
Components(KaiC) x 2
KeywordsTRANSFERASE / clock protein
Function / homologyPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsFuruike, Y. / Akiyama, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal Structure of Designed Clock Protein KaiC
Authors: Furuike, Y. / Akiyama, S.
History
DepositionMay 26, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: KaiC
A: KaiC
D: KaiC
E: KaiC
B: KaiC
C: KaiC
G: KaiC
H: KaiC
K: KaiC
L: KaiC
I: KaiC
J: KaiC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)703,59156
Polymers690,95612
Non-polymers12,63544
Water97354
1
F: KaiC
A: KaiC
D: KaiC
E: KaiC
B: KaiC
C: KaiC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)351,77127
Polymers345,4786
Non-polymers6,29321
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area46620 Å2
ΔGint-230 kcal/mol
Surface area86020 Å2
MethodPISA
2
G: KaiC
H: KaiC
K: KaiC
L: KaiC
I: KaiC
J: KaiC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)351,82029
Polymers345,4786
Non-polymers6,34223
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44600 Å2
ΔGint-240 kcal/mol
Surface area86430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.760, 110.270, 166.890
Angle α, β, γ (deg.)77.97, 87.25, 82.41
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
KaiC


Mass: 57633.023 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: phosphorylated / Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / References: non-specific serine/threonine protein kinase
#2: Protein
KaiC


Mass: 57553.047 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / References: non-specific serine/threonine protein kinase
#3: Chemical...
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.34 Å3/Da / Density % sol: 47.5 %
Crystal growTemperature: 313 K / Method: vapor diffusion / Details: Sodium formate, Sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 20, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.94→48.74 Å / Num. obs: 132294 / % possible obs: 99.5 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.3
Reflection shellResolution: 2.94→3.05 Å / Rmerge(I) obs: 0.51 / Num. unique obs: 12958

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GBL

2gbl


Resolution: 2.94→48.74 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.874 / SU B: 23.728 / SU ML: 0.439 / Cross valid method: THROUGHOUT / ESU R Free: 0.501 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2919 6615 5 %RANDOM
Rwork0.23933 ---
obs0.24189 125679 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.837 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å2-3.53 Å22.94 Å2
2--2.72 Å21.28 Å2
3----4.44 Å2
Refinement stepCycle: 1 / Resolution: 2.94→48.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40387 0 764 54 41205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01141875
X-RAY DIFFRACTIONr_bond_other_d0.0010.01637309
X-RAY DIFFRACTIONr_angle_refined_deg0.6391.65457086
X-RAY DIFFRACTIONr_angle_other_deg0.2381.56684939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.58755591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.2645284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.258105856
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0290.26757
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0250163
X-RAY DIFFRACTIONr_gen_planes_other0.0010.029837
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3937.87422478
X-RAY DIFFRACTIONr_mcbond_other1.3937.87422478
X-RAY DIFFRACTIONr_mcangle_it2.47914.15128031
X-RAY DIFFRACTIONr_mcangle_other2.47914.15128032
X-RAY DIFFRACTIONr_scbond_it1.2287.77219397
X-RAY DIFFRACTIONr_scbond_other1.2287.77219397
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.20314.37129056
X-RAY DIFFRACTIONr_long_range_B_refined4.35471.6844228
X-RAY DIFFRACTIONr_long_range_B_other4.34571.6944210
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.943→3.019 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 477 -
Rwork0.332 9055 -
obs--97.13 %

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