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- PDB-8zn5: Crystal Structure of Designed Clock Protein KaiC -

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Basic information

Entry
Database: PDB / ID: 8zn5
TitleCrystal Structure of Designed Clock Protein KaiC
ComponentsKaiC
KeywordsTRANSFERASE / clock protein
Function / homologyADENOSINE-5'-DIPHOSPHATE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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
B: KaiC
C: KaiC
F: KaiC
A: KaiC
D: KaiC
E: KaiC
G: KaiC
H: KaiC
K: KaiC
L: KaiC
I: KaiC
J: KaiC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)709,70760
Polymers698,87112
Non-polymers10,83648
Water48627
1
B: KaiC
C: KaiC
F: KaiC
A: KaiC
D: KaiC
E: KaiC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,85330
Polymers349,4356
Non-polymers5,41824
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34980 Å2
ΔGint-274 kcal/mol
Surface area94240 Å2
MethodPISA
2
G: KaiC
H: KaiC
K: KaiC
L: KaiC
I: KaiC
J: KaiC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,85330
Polymers349,4356
Non-polymers5,41824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30750 Å2
ΔGint-262 kcal/mol
Surface area102430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.126, 385.574, 108.115
Angle α, β, γ (deg.)90.00, 113.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
KaiC


Mass: 58239.227 Da / Num. of mol.: 12
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
#2: Chemical...
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.55 Å3/Da / Density % sol: 51.84 %
Crystal growTemperature: 313 K / Method: vapor diffusion / Details: Acetic acid 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: Feb 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3→49.35 Å / Num. obs: 138997 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.4
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 1.09 / Num. unique obs: 13900

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Processing

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

2gbl


Resolution: 3.1→49.35 Å / Cor.coef. Fo:Fc: 0.873 / Cor.coef. Fo:Fc free: 0.834 / SU B: 30.877 / SU ML: 0.551 / Cross valid method: THROUGHOUT / ESU R Free: 0.575 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32907 6294 5 %RANDOM
Rwork0.28017 ---
obs0.28262 119652 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.435 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å2-0 Å20.75 Å2
2---0.47 Å20 Å2
3---0.81 Å2
Refinement stepCycle: 1 / Resolution: 3.1→49.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36026 0 672 27 36725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01137321
X-RAY DIFFRACTIONr_bond_other_d0.0010.01631663
X-RAY DIFFRACTIONr_angle_refined_deg0.611.64951028
X-RAY DIFFRACTIONr_angle_other_deg0.2441.56871685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.49355314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.895225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.694104353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0270.26121
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0245579
X-RAY DIFFRACTIONr_gen_planes_other0.0010.028513
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_it1.2718.79621424
X-RAY DIFFRACTIONr_mcbond_other1.2718.79621424
X-RAY DIFFRACTIONr_mcangle_it2.33215.80726682
X-RAY DIFFRACTIONr_mcangle_other2.33215.80726683
X-RAY DIFFRACTIONr_scbond_it0.8458.34815897
X-RAY DIFFRACTIONr_scbond_other0.8458.34815897
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.64815.5424347
X-RAY DIFFRACTIONr_long_range_B_refined4.19981.0639436
X-RAY DIFFRACTIONr_long_range_B_other4.19681.0639430
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 419 -
Rwork0.341 8841 -
obs--99.98 %

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