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- PDB-7q87: Carboxypeptidase T with (S)-3-phenyllactic acid -

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Basic information

Entry
Database: PDB / ID: 7q87
TitleCarboxypeptidase T with (S)-3-phenyllactic acid
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
ALPHA-HYDROXY-BETA-PHENYL-PROPIONIC ACID / Carboxypeptidase T
Similarity search - Component
Biological speciesThermoactinomyces vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.73 Å
AuthorsTimofeev, V.I. / Akparov, V.K. / Shevtsov, M.B. / Kuranova, I.P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Carboxypeptidase T with (S)-3-phenyllactic acid
Authors: Timofeev, V.I. / Akparov, V.K. / Shevtsov, M.B. / Kuranova, I.P.
History
DepositionNov 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)37,37611
Polymers36,6411
Non-polymers73410
Water6,593366
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-83 kcal/mol
Surface area11850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.328, 157.328, 104.132
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-605-

HOH

21A-674-

HOH

31A-837-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Carboxypeptidase T


Mass: 36641.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoactinomyces vulgaris (bacteria) / Gene: cpt / Production host: Escherichia coli (E. coli) / References: UniProt: P29068, carboxypeptidase T

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Non-polymers , 5 types, 376 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-HFA / ALPHA-HYDROXY-BETA-PHENYL-PROPIONIC ACID


Type: L-peptide linking / Mass: 166.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10O3
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: SA 1.4%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.7749 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.73→30 Å / Num. obs: 79136 / % possible obs: 99.98 % / Redundancy: 18.17 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 0.137
Reflection shellResolution: 1.73→1.82 Å / Rmerge(I) obs: 0.43 / Num. unique obs: 11382 / Rrim(I) all: 0.332

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QNV

3qnv


Resolution: 1.73→29.94 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.915 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.051 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1453 3928 5 %RANDOM
Rwork0.1308 ---
obs0.1315 75180 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.31 Å2 / Biso mean: 15.146 Å2 / Biso min: 7.56 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.73→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2581 0 60 366 3007
Biso mean--29.63 30.5 -
Num. residues----323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0132773
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152397
X-RAY DIFFRACTIONr_angle_refined_deg2.1621.6743780
X-RAY DIFFRACTIONr_angle_other_deg1.6821.5975542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2185340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.50723.179151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.74515423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3881513
X-RAY DIFFRACTIONr_chiral_restr0.1380.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023261
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02693
LS refinement shellResolution: 1.73→1.775 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.149 274 -
Rwork0.145 5464 -
all-5738 -
obs--100 %

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