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- PDB-7aqp: T262S, A251S, L254S, L211Q mutant of carboxypeptidase T from Ther... -

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Basic information

Entry
Database: PDB / ID: 7aqp
TitleT262S, A251S, L254S, L211Q mutant of carboxypeptidase T from Thermoactinomyces vulgaris
ComponentsCarboxypeptidase T
KeywordsHYDROLASE / carboxypeptidase
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: 2.6 Å
AuthorsTimofeev, V.I. / Akparov, V.K. / Kuranova, I.P.
CitationJournal: To Be Published
Title: T262S, A251S, L254S, L211Q mutant of carboxypeptidase T from Thermoactinomyces vulgaris
Authors: Timofeev, V.I. / Akparov, V.K. / Kuranova, I.P.
History
DepositionOct 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 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

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Assembly

Deposited unit
A: Carboxypeptidase T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0508
Polymers36,6321
Non-polymers4187
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-127 kcal/mol
Surface area12210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.278, 158.278, 104.610
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-540-

HOH

21A-573-

HOH

31A-605-

HOH

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Components

#1: Protein Carboxypeptidase T


Mass: 36632.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoactinomyces vulgaris (bacteria) / Gene: cpt / Production host: Thermoactinomyces vulgaris (bacteria) / References: UniProt: P29068, carboxypeptidase T
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 1.6 Ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 23589 / % possible obs: 97.9 % / Redundancy: 9.94 % / Rmerge(I) obs: 0.169 / Net I/σ(I): 3.774
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 9.64 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 2.04 / Num. unique obs: 3397 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QNV

3qnv


Resolution: 2.6→29.91 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.941 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1192 5.1 %RANDOM
Rwork0.164 ---
obs0.166 22397 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 147.23 Å2 / Biso mean: 33.23 Å2 / Biso min: 11.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.05 Å2
Refinement stepCycle: final / Resolution: 2.6→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2580 0 15 128 2723
Biso mean--66.43 40.74 -
Num. residues----323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132673
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172248
X-RAY DIFFRACTIONr_angle_refined_deg1.6881.6533636
X-RAY DIFFRACTIONr_angle_other_deg1.4021.5735246
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1645324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.44523.113151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.93915414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0811513
X-RAY DIFFRACTIONr_chiral_restr0.0780.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023052
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02591
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_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 92 -
Rwork0.259 1613 -
all-1705 -
obs--98.38 %

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