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- PDB-9k7w: Crystal structure of designed nickel-induced homotrimer C3-Ni1-HH*3-18 -

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Basic information

Entry
Database: PDB / ID: 9k7w
TitleCrystal structure of designed nickel-induced homotrimer C3-Ni1-HH*3-18
ComponentsC3-Ni1-HH*3-18
KeywordsMETAL BINDING PROTEIN / trimer / nickel-binding protein
Function / homologyNICKEL (II) ION / NITRATE ION
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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: C3-Ni1-HH*3-18
B: C3-Ni1-HH*3-18
C: C3-Ni1-HH*3-18
D: C3-Ni1-HH*3-18
E: C3-Ni1-HH*3-18
F: C3-Ni1-HH*3-18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,69912
Polymers75,3336
Non-polymers3656
Water7,278404
1
A: C3-Ni1-HH*3-18
B: C3-Ni1-HH*3-18
C: C3-Ni1-HH*3-18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8496
Polymers37,6673
Non-polymers1833
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-18 kcal/mol
Surface area12740 Å2
MethodPISA
2
D: C3-Ni1-HH*3-18
E: C3-Ni1-HH*3-18
F: C3-Ni1-HH*3-18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8496
Polymers37,6673
Non-polymers1833
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-21 kcal/mol
Surface area12950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.464, 77.921, 68.417
Angle α, β, γ (deg.)90.00, 95.26, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
C3-Ni1-HH*3-18


Mass: 12555.532 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / 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 % sol: 34.71 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 20% (w/v) PEG 3350, 200 mM Ammonium nitrate

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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: Jun 5, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2.1→29.97 Å / Num. obs: 32684 / % possible obs: 96.36 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.06257 / Net I/σ(I): 15.03
Reflection shellResolution: 2.1→2.175 Å / Rmerge(I) obs: 0.1812 / Num. unique obs: 3061

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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: 2.1→29.97 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 28.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2934 1661 5.27 %
Rwork0.2162 --
obs0.2201 31545 96.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4206 0 17 404 4627
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_d1.047
X-RAY DIFFRACTIONf_dihedral_angle_d6.276
X-RAY DIFFRACTIONf_chiral_restr0.048
X-RAY DIFFRACTIONf_plane_restr0.005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.160.33751290.22372408X-RAY DIFFRACTION94
2.16-2.230.33271410.21732450X-RAY DIFFRACTION96
2.23-2.310.27371340.21882415X-RAY DIFFRACTION94
2.31-2.40.28191360.22122462X-RAY DIFFRACTION95
2.4-2.510.31221350.22512452X-RAY DIFFRACTION95
2.51-2.650.3331380.22282463X-RAY DIFFRACTION96
2.65-2.810.3171380.22542476X-RAY DIFFRACTION96
2.81-3.030.31521360.23472466X-RAY DIFFRACTION96
3.03-3.330.31941410.22182564X-RAY DIFFRACTION99
3.33-3.810.23931450.19882566X-RAY DIFFRACTION99
3.81-4.80.27551410.19112553X-RAY DIFFRACTION98
4.8-29.970.28641470.23052609X-RAY DIFFRACTION99

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