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- PDB-8qvo: L211Q, L254N, T262G mutant of carboxypeptidase T from Thermoactin... -

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Basic information

Entry
Database: PDB / ID: 8qvo
TitleL211Q, L254N, T262G mutant of carboxypeptidase T from Thermoactinomyces vulgaris
ComponentsCarboxypeptidase T
KeywordsHYDROLASE
Function / homology
Function and homology information


carboxypeptidase T / metallocarboxypeptidase activity / proteolysis / extracellular space / zinc ion binding
Similarity search - Function
Carboxypeptidase T / Zinc carboxypeptidases, zinc-binding region 2 signature. / Zinc carboxypeptidases, zinc-binding region 1 signature. / Zn_pept / Zinc carboxypeptidase / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A
Similarity search - Domain/homology
Biological speciesThermoactinomyces vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsTimofeev, V.I. / Dorovatovskii, P.V. / Lazarenko, V.A. / Akparov, V.K. / Kuranova, I.P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: L211Q, L254N, T262G mutant of carboxypeptidase T from Thermoactinomyces vulgaris
Authors: Timofeev, V.I. / Dorovatovskii, P.V. / Lazarenko, V.A. / Akparov, V.K. / Kuranova, I.P.
History
DepositionOct 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxypeptidase T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,16710
Polymers36,6131
Non-polymers5549
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint-141 kcal/mol
Surface area12170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.085, 158.085, 104.589
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-635-

HOH

21A-670-

HOH

31A-837-

HOH

41A-887-

HOH

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Components

#1: Protein Carboxypeptidase T


Mass: 36613.141 Da / Num. of mol.: 1 / Mutation: L211Q,L254N,T262G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoactinomyces vulgaris (bacteria) / Gene: cpt / Production host: Thermoactinomyces vulgaris (bacteria) / References: UniProt: P29068
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.4 SA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.75268 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Oct 2, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75268 Å / Relative weight: 1
ReflectionResolution: 1.96→30 Å / Num. obs: 110357 / % possible obs: 99.97 % / Redundancy: 12.09 % / Rmerge(I) obs: 0.11 / Rrim(I) all: 0.115 / Net I/σ(I): 5.8757
Reflection shellResolution: 1.96→2.07 Å / Redundancy: 9.41 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 15903 / Rrim(I) all: 0.376 / % possible all: 99.99

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→28.91 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.51 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1655 2714 4.9 %RANDOM
Rwork0.14552 ---
obs0.14649 52826 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.85 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.96→28.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2579 0 21 418 3018
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132671
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152318
X-RAY DIFFRACTIONr_angle_refined_deg1.7741.6533634
X-RAY DIFFRACTIONr_angle_other_deg1.5971.585347
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4245324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.07123.224152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99815412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9821513
X-RAY DIFFRACTIONr_chiral_restr0.0970.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023113
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02661
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_it1.3281.3491296
X-RAY DIFFRACTIONr_mcbond_other1.2881.3461295
X-RAY DIFFRACTIONr_mcangle_it1.7882.011620
X-RAY DIFFRACTIONr_mcangle_other1.7992.0121621
X-RAY DIFFRACTIONr_scbond_it2.3871.5251373
X-RAY DIFFRACTIONr_scbond_other2.2861.5051361
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.432.1831997
X-RAY DIFFRACTIONr_long_range_B_refined5.21917.4323351
X-RAY DIFFRACTIONr_long_range_B_other4.74816.5333245
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.96→2.011 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.175 198 -
Rwork0.149 3833 -
obs--100 %

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