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- PDB-9ju4: Crystal structure of the Thermotoga maritima cold shock protein m... -

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Basic information

Entry
Database: PDB / ID: 9ju4
TitleCrystal structure of the Thermotoga maritima cold shock protein mutant Est#13 in complex with AacEst
Components
  • Alpha/beta hydrolase fold-3 domain protein
  • The Thermotoga maritima cold shock protein mutant binding to AacEst
KeywordsPROTEIN BINDING / Antibody-mimics / Cold shock protein / Refolding / Heat sterilization / Freeze-drying
Function / homologyshort-chain carboxylesterase activity / : / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold / DI(HYDROXYETHYL)ETHER / phenylmethanesulfonic acid / Alpha/beta hydrolase fold-3 domain protein
Function and homology information
Biological speciesAlicyclobacillus acidocaldarius (bacteria)
Thermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTanaka, S.-i. / Amesaka, H.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21K05386 Japan
Japan Society for the Promotion of Science (JSPS)23H04559 Japan
Japan Society for the Promotion of Science (JSPS)24K08717 Japan
Japan Society for the Promotion of Science (JSPS)23KJ1820 Japan
CitationJournal: Protein Sci. / Year: 2025
Title: Heat-sterilizable antibody mimics designed on the cold shock protein scaffold from hyperthermophile Thermotoga maritima.
Authors: Amesaka, H. / Tachibana, M. / Hara, M. / Toya, S. / Nakagawa, H. / Matsumura, H. / Hirata, A. / Fujihashi, M. / Takano, K. / Tanaka, S.I.
History
DepositionOct 7, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha/beta hydrolase fold-3 domain protein
B: The Thermotoga maritima cold shock protein mutant binding to AacEst
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0875
Polymers41,7162
Non-polymers3703
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-0 kcal/mol
Surface area15120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.820, 46.650, 101.260
Angle α, β, γ (deg.)90.00, 93.99, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-621-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Alpha/beta hydrolase fold-3 domain protein


Mass: 34338.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alicyclobacillus acidocaldarius (bacteria)
Gene: Aaci_2875 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C8WUR3
#2: Protein The Thermotoga maritima cold shock protein mutant binding to AacEst


Mass: 7377.190 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 4 types, 179 molecules

#3: Chemical ChemComp-PMS / phenylmethanesulfonic acid


Mass: 172.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.59 Å3/Da / Density % sol: 54.43 % / Description: Needle-like crystals
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M sodium citrate, pH 5.0, and 20% (W/V) PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→46.65 Å / Num. obs: 28793 / % possible obs: 99.2 % / Redundancy: 4.38 % / CC1/2: 0.999 / Net I/σ(I): 11.13
Reflection shellResolution: 1.52→1.61 Å / Num. unique obs: 10348 / CC1/2: 0.54

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→46.65 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.207 886 3.08 %
Rwork0.1695 --
obs0.1707 28793 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→46.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2839 0 23 176 3038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082939
X-RAY DIFFRACTIONf_angle_d0.8733995
X-RAY DIFFRACTIONf_dihedral_angle_d7.288400
X-RAY DIFFRACTIONf_chiral_restr0.055424
X-RAY DIFFRACTIONf_plane_restr0.005524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.130.20411460.17094653X-RAY DIFFRACTION100
2.13-2.290.20081450.17744618X-RAY DIFFRACTION99
2.29-2.520.23921400.17774649X-RAY DIFFRACTION99
2.52-2.880.21881520.18234644X-RAY DIFFRACTION99
2.88-3.630.19961480.17364669X-RAY DIFFRACTION99
3.63-46.650.19991550.15684674X-RAY DIFFRACTION97

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