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- PDB-9k5h: Crystal structure of designed zinc-induced homodimer C2-Zn2-HEHE-2 -

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Basic information

Entry
Database: PDB / ID: 9k5h
TitleCrystal structure of designed zinc-induced homodimer C2-Zn2-HEHE-2
ComponentsC2-Zn2-HEHE-2
KeywordsMETAL BINDING PROTEIN / Dimer / Zinc-binding protein
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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-Zn2-HEHE-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3793
Polymers10,2491
Non-polymers1312
Water1,15364
1
A: C2-Zn2-HEHE-2
hetero molecules

A: C2-Zn2-HEHE-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7596
Polymers20,4972
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Buried area2320 Å2
ΔGint-149 kcal/mol
Surface area7350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.611, 47.611, 54.164
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-201-

HOH

21A-209-

HOH

31A-212-

HOH

41A-260-

HOH

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Components

#1: Protein C2-Zn2-HEHE-2


Mass: 10248.548 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: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 64 / 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 pH 7, 30% v/v Jeff ED-2001

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: May 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→23.81 Å / Num. obs: 6169 / % possible obs: 99.84 % / Redundancy: 10 % / Rmerge(I) obs: 0.03474 / Net I/σ(I): 45.4
Reflection shellResolution: 1.8→1.864 Å / Rmerge(I) obs: 0.227 / Num. unique obs: 597

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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: 1.8→23.81 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2402 617 10 %
Rwork0.1869 --
obs0.1921 6167 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→23.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms569 0 2 64 635
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.875
X-RAY DIFFRACTIONf_dihedral_angle_d4.414
X-RAY DIFFRACTIONf_chiral_restr0.045
X-RAY DIFFRACTIONf_plane_restr0.01
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.980.22391490.18041342X-RAY DIFFRACTION100
1.98-2.270.24711510.18051362X-RAY DIFFRACTION100
2.27-2.860.25751530.19551376X-RAY DIFFRACTION100
2.86-23.810.23391640.18631470X-RAY DIFFRACTION100

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