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- PDB-9k7x: Crystal structure of designed calcium-induced homotrimer C3-Ca1-D... -

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Basic information

Entry
Database: PDB / ID: 9k7x
TitleCrystal structure of designed calcium-induced homotrimer C3-Ca1-DN*3-20
ComponentsC3-Ca1-DN*3-20
KeywordsMETAL BINDING PROTEIN / trimer / calcium-binding protein
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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-Ca1-DN*3-20
B: C3-Ca1-DN*3-20
C: C3-Ca1-DN*3-20
D: C3-Ca1-DN*3-20
E: C3-Ca1-DN*3-20
F: C3-Ca1-DN*3-20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,07510
Polymers74,8326
Non-polymers2424
Water5,765320
1
A: C3-Ca1-DN*3-20
D: C3-Ca1-DN*3-20
E: C3-Ca1-DN*3-20
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6186
Polymers37,4163
Non-polymers2023
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-27 kcal/mol
Surface area11660 Å2
MethodPISA
2
C: C3-Ca1-DN*3-20
F: C3-Ca1-DN*3-20
hetero molecules

B: C3-Ca1-DN*3-20


Theoretical massNumber of molelcules
Total (without water)37,4564
Polymers37,4163
Non-polymers401
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area4940 Å2
ΔGint-27 kcal/mol
Surface area11940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.614, 77.562, 82.814
Angle α, β, γ (deg.)90.00, 92.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
C3-Ca1-DN*3-20


Mass: 12472.063 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 0.1M Tris pH 8.0 37% PEG400

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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 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54184 Å / Relative weight: 1
ReflectionResolution: 2→27.11 Å / Num. obs: 29342 / % possible obs: 97.52 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.08063 / Net I/σ(I): 15.89
Reflection shellResolution: 2→2.071 Å / Rmerge(I) obs: 0.4368 / Num. unique obs: 2818

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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→27.11 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 21.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2274 1966 6.8 %
Rwork0.1721 --
obs0.1759 28916 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→27.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4142 0 11 320 4473
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.773
X-RAY DIFFRACTIONf_dihedral_angle_d4.505
X-RAY DIFFRACTIONf_chiral_restr0.04
X-RAY DIFFRACTIONf_plane_restr0.005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.24361490.16851841X-RAY DIFFRACTION94
2.05-2.110.24521180.17551903X-RAY DIFFRACTION97
2.11-2.170.22161480.16631973X-RAY DIFFRACTION98
2.17-2.240.22121500.16421896X-RAY DIFFRACTION99
2.24-2.320.22531470.16061952X-RAY DIFFRACTION98
2.32-2.410.22891450.16151917X-RAY DIFFRACTION99
2.41-2.520.231280.17111962X-RAY DIFFRACTION99
2.52-2.650.22031360.16761965X-RAY DIFFRACTION99
2.65-2.820.22771450.17581897X-RAY DIFFRACTION98
2.82-3.040.24491290.18421946X-RAY DIFFRACTION97
3.04-3.340.26391470.16991936X-RAY DIFFRACTION98
3.34-3.820.18381410.16481954X-RAY DIFFRACTION98
3.82-4.810.18051400.15581914X-RAY DIFFRACTION97
4.81-27.110.2861430.20961894X-RAY DIFFRACTION94

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