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- PDB-9k4q: Crystal structure of designed zinc-induced homodimer C2-Zn1-HEHE-2 -

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Basic information

Entry
Database: PDB / ID: 9k4q
TitleCrystal structure of designed zinc-induced homodimer C2-Zn1-HEHE-2
ComponentsC2-Zn1-HEHE-2
KeywordsMETAL BINDING PROTEIN / Dimer / Zinc-binding protein
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: C2-Zn1-HEHE-2
C: C2-Zn1-HEHE-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0873
Polymers26,0222
Non-polymers651
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-42 kcal/mol
Surface area9410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.643, 93.272, 31.779
Angle α, β, γ (deg.)90.00, 118.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein C2-Zn1-HEHE-2


Mass: 13010.884 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 0.1 M HEPES pH7.5, 22% PEG400, 0.2 M NaCl

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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: Apr 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2→27.87 Å / Num. obs: 10526 / % possible obs: 99.44 % / Redundancy: 3 % / Rmerge(I) obs: 0.03454 / Net I/σ(I): 21
Reflection shellResolution: 2→2.072 Å / Rmerge(I) obs: 0.1201 / Num. unique obs: 1024

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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: 2→27.87 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 24.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2478 1062 10.09 %
Rwork0.1901 --
obs0.196 10524 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→27.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1460 0 1 99 1560
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.779
X-RAY DIFFRACTIONf_dihedral_angle_d4.212
X-RAY DIFFRACTIONf_chiral_restr0.042
X-RAY DIFFRACTIONf_plane_restr0.005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.090.2551280.17861149X-RAY DIFFRACTION98
2.09-2.20.28661250.19221166X-RAY DIFFRACTION100
2.2-2.340.2721440.19651207X-RAY DIFFRACTION100
2.34-2.520.21771230.18511185X-RAY DIFFRACTION100
2.52-2.770.28841380.19061180X-RAY DIFFRACTION100
2.77-3.170.27531370.19831198X-RAY DIFFRACTION100
3.17-40.2261230.18211189X-RAY DIFFRACTION100
4-27.870.22511440.1941188X-RAY DIFFRACTION99

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