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- PDB-9gzg: Crystal structure of CTPR4E4 mutant -

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Basic information

Entry
Database: PDB / ID: 9gzg
TitleCrystal structure of CTPR4E4 mutant
ComponentsEngineered CTPR protein with glutamic acids for conductivity
KeywordsDE NOVO PROTEIN / CTPR / protein engineering / conductivity.
Function / homologyMALONIC ACID / TRIETHYLENE GLYCOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsLiutkus, M. / Cortajarena, A.L.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)964593European Union
CitationJournal: To Be Published
Title: Crystal structure of CTPR4E4 mutant
Authors: Liutkus, M. / Cortajarena, A.L.
History
DepositionOct 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Engineered CTPR protein with glutamic acids for conductivity
B: Engineered CTPR protein with glutamic acids for conductivity
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4595
Polymers35,7902
Non-polymers6693
Water1,33374
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint5 kcal/mol
Surface area15280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.915, 73.514, 40.778
Angle α, β, γ (deg.)90.00, 98.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Engineered CTPR protein with glutamic acids for conductivity


Mass: 17894.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
#2: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.44 Å3/Da / Density % sol: 49.63 % / Description: needles
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 8% v/v Tacsimate pH4, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.47→52.44 Å / Num. obs: 35904 / % possible obs: 86.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 23.6 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.046 / Rrim(I) all: 0.108 / Net I/σ(I): 1.41
Reflection shellResolution: 1.47→1.65 Å / Redundancy: 4.2 % / Num. unique obs: 1795 / CC1/2: 0.418 / % possible all: 37.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
autoPROC1.0.5data scaling
MOLREP11.9.02phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→52.44 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / SU B: 2.445 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23069 1805 5 %RANDOM
Rwork0.19577 ---
obs0.19753 34099 68.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.054 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å2-0.18 Å2
2--0.08 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.47→52.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2530 0 45 74 2649
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122635
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162267
X-RAY DIFFRACTIONr_angle_refined_deg1.691.8763544
X-RAY DIFFRACTIONr_angle_other_deg0.5761.7895289
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.515308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.95458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.15910442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0870.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023177
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02571
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2832.5131232
X-RAY DIFFRACTIONr_mcbond_other2.2792.5071231
X-RAY DIFFRACTIONr_mcangle_it3.1854.51537
X-RAY DIFFRACTIONr_mcangle_other3.1864.5071538
X-RAY DIFFRACTIONr_scbond_it4.6293.2541403
X-RAY DIFFRACTIONr_scbond_other4.6273.2541404
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4555.6192007
X-RAY DIFFRACTIONr_long_range_B_refined8.4829.673125
X-RAY DIFFRACTIONr_long_range_B_other8.47929.43124
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.47→1.508 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 3 -
Rwork0.324 68 -
obs--1.83 %

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