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- PDB-9k6o: Crystal structure of designed zinc-induced homopentamer C5-Zn1-HEHE-1 -

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Basic information

Entry
Database: PDB / ID: 9k6o
TitleCrystal structure of designed zinc-induced homopentamer C5-Zn1-HEHE-1
ComponentsC5-Zn1-HEHE-1
KeywordsMETAL BINDING PROTEIN / pentamer / Zinc-binding protein
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 22, 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

Downloads & links

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Assembly

Deposited unit
A: C5-Zn1-HEHE-1
B: C5-Zn1-HEHE-1
C: C5-Zn1-HEHE-1
D: C5-Zn1-HEHE-1
E: C5-Zn1-HEHE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,49910
Polymers63,1725
Non-polymers3275
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5660 Å2
ΔGint-210 kcal/mol
Surface area20610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.135, 108.329, 54.577
Angle α, β, γ (deg.)90.00, 95.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
C5-Zn1-HEHE-1


Mass: 12634.456 Da / Num. of mol.: 5
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.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 0.02 M Calcium chloride dihydrate, 0.1 M Sodium acetate trihydrate pH 4.6, 30% v/v (+/-)-2-Methyl-2,4-pentanediol

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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 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.15→28.7 Å / Num. obs: 23952 / % possible obs: 96.73 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.04439 / Net I/σ(I): 22.35
Reflection shellResolution: 2.15→2.227 Å / Rmerge(I) obs: 0.2833 / Num. unique obs: 2240

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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→28.7 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 24.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2412 1564 6.73 %
Rwork0.1883 --
obs0.1918 23227 96.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→28.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3596 0 5 222 3823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.809
X-RAY DIFFRACTIONf_dihedral_angle_d4.746
X-RAY DIFFRACTIONf_chiral_restr0.049
X-RAY DIFFRACTIONf_plane_restr0.006612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.220.30831370.21881891X-RAY DIFFRACTION93
2.22-2.30.22921390.20651919X-RAY DIFFRACTION94
2.3-2.390.28281410.20541945X-RAY DIFFRACTION95
2.39-2.50.30451370.19921921X-RAY DIFFRACTION96
2.5-2.630.25481430.21361962X-RAY DIFFRACTION97
2.63-2.80.2491410.21081965X-RAY DIFFRACTION97
2.8-3.010.27991430.20451983X-RAY DIFFRACTION97
3.01-3.310.23921460.20761997X-RAY DIFFRACTION99
3.31-3.790.2861450.19232035X-RAY DIFFRACTION99
3.79-4.770.20791470.15972019X-RAY DIFFRACTION99
4.78-28.70.1881450.16292026X-RAY DIFFRACTION98

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