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- PDB-8zn7: Crystal Structure of Designed Clock Protein KaiC -

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Basic information

Entry
Database: PDB / ID: 8zn7
TitleCrystal Structure of Designed Clock Protein KaiC
ComponentsKaiC
KeywordsTRANSFERASE / clock protein
Function / homologyPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 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
D: KaiC
E: KaiC
B: KaiC
C: KaiC
F: KaiC
A: KaiC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)348,92730
Polymers342,5616
Non-polymers6,36624
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area46170 Å2
ΔGint-240 kcal/mol
Surface area85600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.977, 175.183, 94.774
Angle α, β, γ (deg.)90.00, 96.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
KaiC


Mass: 57093.547 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growTemperature: 313 K / Method: vapor diffusion / pH: 7 / Details: Tris-HCl KCl 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: Dec 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.54→49.19 Å / Num. obs: 98128 / % possible obs: 99.7 % / Redundancy: 7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.3
Reflection shellResolution: 2.54→2.63 Å / Rmerge(I) obs: 0.71 / Num. unique obs: 9618

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Processing

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

2gbl


Resolution: 2.54→49.19 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.913 / SU B: 13.219 / SU ML: 0.288 / Cross valid method: THROUGHOUT / ESU R: 0.861 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27249 4907 5 %RANDOM
Rwork0.22469 ---
obs0.22708 93220 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.283 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å22.64 Å2
2--0.54 Å20 Å2
3----0.9 Å2
Refinement stepCycle: 1 / Resolution: 2.54→49.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20443 0 384 104 20931
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01221203
X-RAY DIFFRACTIONr_bond_other_d0.0010.01619378
X-RAY DIFFRACTIONr_angle_refined_deg0.7721.65428842
X-RAY DIFFRACTIONr_angle_other_deg0.2751.56844189
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.16852773
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.8215149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.164103169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0350.23402
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0225053
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024939
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_it2.2846.59711146
X-RAY DIFFRACTIONr_mcbond_other2.2836.59711146
X-RAY DIFFRACTIONr_mcangle_it3.77911.85913901
X-RAY DIFFRACTIONr_mcangle_other3.77911.85913902
X-RAY DIFFRACTIONr_scbond_it2.4126.64710057
X-RAY DIFFRACTIONr_scbond_other2.4126.64710057
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.11512.21514942
X-RAY DIFFRACTIONr_long_range_B_refined6.36860.2922259
X-RAY DIFFRACTIONr_long_range_B_other6.36860.322250
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.54→2.601 Å
RfactorNum. reflection% reflection
Rfree0.333 351 -
Rwork0.295 6659 -
obs--97.19 %

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