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- PDB-9k7t: Crystal structure of designed zinc-induced homotetramer C4-Zn1-HEHE-1 -

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Basic information

Entry
Database: PDB / ID: 9k7t
TitleCrystal structure of designed zinc-induced homotetramer C4-Zn1-HEHE-1
ComponentsC4-Zn1-HEHE-1
KeywordsMETAL BINDING PROTEIN / tetramer / Zinc-binding protein
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.52 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: C4-Zn1-HEHE-1
B: C4-Zn1-HEHE-1
C: C4-Zn1-HEHE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4336
Polymers38,2373
Non-polymers1963
Water2,090116
1
A: C4-Zn1-HEHE-1
hetero molecules

A: C4-Zn1-HEHE-1
hetero molecules

A: C4-Zn1-HEHE-1
hetero molecules

A: C4-Zn1-HEHE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2448
Polymers50,9834
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area5380 Å2
ΔGint-168 kcal/mol
Surface area16500 Å2
MethodPISA
2
B: C4-Zn1-HEHE-1
hetero molecules

B: C4-Zn1-HEHE-1
hetero molecules

B: C4-Zn1-HEHE-1
hetero molecules

B: C4-Zn1-HEHE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2448
Polymers50,9834
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area4740 Å2
ΔGint-178 kcal/mol
Surface area16950 Å2
MethodPISA
3
C: C4-Zn1-HEHE-1
hetero molecules

C: C4-Zn1-HEHE-1
hetero molecules

C: C4-Zn1-HEHE-1
hetero molecules

C: C4-Zn1-HEHE-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2448
Polymers50,9834
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area4460 Å2
ΔGint-187 kcal/mol
Surface area17030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.506, 67.506, 72.269
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Components on special symmetry positions
IDModelComponents
11A-210-

HOH

21A-234-

HOH

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Components

#1: Protein C4-Zn1-HEHE-1


Mass: 12745.664 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.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.15 Å3/Da / Density % sol: 42.88 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 2.4 M Sodium malonate dibasic

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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: Feb 28, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.52→30.19 Å / Num. obs: 11060 / % possible obs: 98.19 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.06302 / Net I/σ(I): 25.26
Reflection shellResolution: 2.52→2.61 Å / Rmerge(I) obs: 0.1772 / Num. unique obs: 1023

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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: 2.52→30.19 Å / Cross valid method: FREE R-VALUE / σ(F): 1.14 / Phase error: 30.73 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2481 975 8.96 %
Rwork0.1854 --
obs0.1946 10881 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.52→30.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2101 0 3 116 2220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.878
X-RAY DIFFRACTIONf_dihedral_angle_d4.954277
X-RAY DIFFRACTIONf_chiral_restr0.041337
X-RAY DIFFRACTIONf_plane_restr0.007356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.650.37781280.23771353X-RAY DIFFRACTION86
2.65-2.820.32371290.22161386X-RAY DIFFRACTION89
2.82-3.040.29021470.21171417X-RAY DIFFRACTION90
3.04-3.340.2641330.20481429X-RAY DIFFRACTION91
3.34-3.820.23331490.17561429X-RAY DIFFRACTION90
3.83-4.810.17671260.14681439X-RAY DIFFRACTION91
4.82-30.190.26071550.19391461X-RAY DIFFRACTION90

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