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- PDB-9k7u: Crystal structure of designed zinc-induced heterodimer Heter-Zn2-... -

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Basic information

Entry
Database: PDB / ID: 9k7u
TitleCrystal structure of designed zinc-induced heterodimer Heter-Zn2-HEHE-22
Components
  • Heter-Zn2-HEHE-22A
  • Heter-Zn2-HEHE-22B
KeywordsMETAL BINDING PROTEIN / Zinc-binding protein
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsQu, Y.N. / Cao, L.X.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: To Be Published
Title: De novo design of metal ion regulated protein assemblies
Authors: Qu, Y.N. / Cao, L.X.
History
DepositionOct 24, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heter-Zn2-HEHE-22A
B: Heter-Zn2-HEHE-22B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8124
Polymers26,6812
Non-polymers1312
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-89 kcal/mol
Surface area9150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.879, 60.879, 91.668
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-343-

HOH

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Components

#1: Protein Heter-Zn2-HEHE-22A


Mass: 17581.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: Protein Heter-Zn2-HEHE-22B


Mass: 9100.302 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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

Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54184 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Mar 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 1.9→30.44 Å / Num. obs: 14176 / % possible obs: 99.96 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.06318 / Net I/σ(I): 30.21
Reflection shellResolution: 1.9→1.968 Å / Rmerge(I) obs: 0.2867 / Num. unique obs: 1390

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RoseTTAFold

Resolution: 1.9→30.44 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2121 1418 10 %
Rwork0.1705 --
obs0.1747 14176 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→30.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1507 0 0 199 1706
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.881
X-RAY DIFFRACTIONf_dihedral_angle_d5.268
X-RAY DIFFRACTIONf_chiral_restr0.05
X-RAY DIFFRACTIONf_plane_restr0.01
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.970.31151390.20841251X-RAY DIFFRACTION100
1.97-2.050.23471360.16191232X-RAY DIFFRACTION100
2.05-2.140.20891390.15251241X-RAY DIFFRACTION100
2.14-2.250.18211410.1551267X-RAY DIFFRACTION100
2.25-2.390.19291380.16111248X-RAY DIFFRACTION100
2.39-2.580.22431400.1631262X-RAY DIFFRACTION100
2.58-2.840.22671420.17531272X-RAY DIFFRACTION100
2.84-3.250.18821420.17461284X-RAY DIFFRACTION100
3.25-4.090.17051450.16041310X-RAY DIFFRACTION100
4.09-30.440.24851560.18861391X-RAY DIFFRACTION100

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