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- PDB-9k5p: Crystal structure of designed zinc-induced homotrimer C3-Zn2-HEHE-19 -

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Basic information

Entry
Database: PDB / ID: 9k5p
TitleCrystal structure of designed zinc-induced homotrimer C3-Zn2-HEHE-19
ComponentsC3-Zn2-HEHE-19
KeywordsMETAL BINDING PROTEIN / trimer / Zinc-binding protein
Function / homologyNITRATE ION
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 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: C3-Zn2-HEHE-19
B: C3-Zn2-HEHE-19
C: C3-Zn2-HEHE-19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,49213
Polymers37,8523
Non-polymers64010
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-247 kcal/mol
Surface area14120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.767, 76.767, 118.278
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein C3-Zn2-HEHE-19


Mass: 12617.260 Da / Num. of mol.: 3
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.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.3 Å3/Da / Density % sol: 46.56 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium acetate trihydrate pH 4.5, 2.0 M Ammonium sulfate

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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: 2.15→29.57 Å / Num. obs: 19879 / % possible obs: 99.76 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.05628 / Net I/σ(I): 27.82
Reflection shellResolution: 2.15→2.227 Å / Rmerge(I) obs: 0.2857 / Num. unique obs: 1929

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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: 2.15→29.57 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2783 1619 8.16 %
Rwork0.2169 --
obs0.2218 19849 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2079 0 22 119 2220
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.782
X-RAY DIFFRACTIONf_dihedral_angle_d4.382
X-RAY DIFFRACTIONf_chiral_restr0.042
X-RAY DIFFRACTIONf_plane_restr0.007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.210.32381320.24161480X-RAY DIFFRACTION100
2.21-2.280.35151310.27081485X-RAY DIFFRACTION100
2.28-2.370.2691310.22251483X-RAY DIFFRACTION100
2.37-2.460.26641320.24881483X-RAY DIFFRACTION100
2.46-2.570.30841340.23781510X-RAY DIFFRACTION100
2.57-2.710.30751330.24371492X-RAY DIFFRACTION100
2.71-2.880.29651330.23781502X-RAY DIFFRACTION100
2.88-3.10.30761340.2331505X-RAY DIFFRACTION100
3.1-3.410.27521360.21481533X-RAY DIFFRACTION100
3.41-3.90.28581370.1941539X-RAY DIFFRACTION100
3.9-4.910.241380.18791559X-RAY DIFFRACTION100
4.92-29.570.2571480.21131659X-RAY DIFFRACTION100

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