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- PDB-9v59: Crystal structure of calcium indicator WHaloCaMP1a labeled with B... -

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Basic information

Entry
Database: PDB / ID: 9v59
TitleCrystal structure of calcium indicator WHaloCaMP1a labeled with BD566-HTL substrate
ComponentsWHaloCaMP1a
KeywordsBIOSYNTHETIC PROTEIN / calcium indicator
Function / homology: / alpha-D-glucopyranose
Function and homology information
Biological speciesEscherichia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.175 Å
AuthorsZhang, K. / Chen, Z.X.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2021YFF0502904 China
National Natural Science Foundation of China (NSFC)W2412031 China
CitationJournal: To Be Published
Title: Crystal strcture of calcium indicator WHaloCaMP1a labeled with BD566-HTL substrate
Authors: Zhang, K.
History
DepositionMay 25, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: WHaloCaMP1a
B: WHaloCaMP1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,17723
Polymers106,6842
Non-polymers3,49321
Water7,062392
1
A: WHaloCaMP1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,17812
Polymers53,3421
Non-polymers1,83611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-12 kcal/mol
Surface area18810 Å2
MethodPISA
2
B: WHaloCaMP1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,99811
Polymers53,3421
Non-polymers1,65610
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-13 kcal/mol
Surface area18740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.936, 94.184, 76.041
Angle α, β, γ (deg.)90, 101.34, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Sugars , 2 types, 11 molecules AB

#1: Protein WHaloCaMP1a


Mass: 53341.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia (bacteria) / Production host: Escherichia (bacteria)
#2: Sugar
ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 404 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-A1EQX / 2-[3,6-bis[(1R,5S)-3-oxa-8-azabicyclo[3.2.1]octan-8-yl]-1H-xanthen-9-yl]-4-[2-(2-hexoxyethoxy)ethylcarbamoyl]benzoic acid


Mass: 739.896 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C43H53N3O8
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.07 Å3/Da / Density % sol: 40.69 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: MES, Ammonium acetate, PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: STFC Large Pixel Detector / Detector: PIXEL / Date: Nov 30, 2024
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 42186 / % possible obs: 92.96 % / Redundancy: 4.1 % / CC1/2: 0.982 / Rpim(I) all: 0.141 / Net I/σ(I): 8.71
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.801 / Mean I/σ(I) obs: 3.35 / Num. unique obs: 2184 / CC1/2: 0.492 / Rpim(I) all: 0.576 / Rrim(I) all: 0.992 / % possible all: 48.77

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Processing

Software
NameVersionClassification
PHENIX1.16_3549: ???refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.175→32.795 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2548 1982 -
Rwork0.2053 --
obs0.2075 41853 92.99 %
Refinement stepCycle: LAST / Resolution: 2.175→32.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7174 0 154 392 7720
LS refinement shellResolution: 2.175→2.253 Å
RfactorNum. reflection% reflection
Rfree0.3007 --
Rwork0.2499 --
obs-2185 48.77 %
Refinement TLS params.Origin x: 12.2722 Å / Origin y: 5.1577 Å / Origin z: 3.5866 Å
111213212223313233
T0.093 Å2-0.036 Å20.0105 Å2-0.1076 Å20.0263 Å2--0.1208 Å2
L0.5506 °2-0.1465 °2-0.1125 °2-0.5104 °20.0701 °2--0.6535 °2
S0.0063 Å °-0.0458 Å °0.0201 Å °-0.0458 Å °0.0011 Å °0.078 Å °0.0201 Å °0.078 Å °-0.0031 Å °
Refinement TLS groupSelection details: all

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